It didn't take long before the standard Roman Catholic answer appeared.* According to many Roman Catholics, Luther removed the Apocrypha because it disagreed with his theology. For instance, 2 Maccabees 12:46 [Open in Logos Bible Software (if available)] teaches such things like Purgatory, and since Luther didn't believe in Purgatory, he removed it. The second part of this Roman Catholic argument is that Luther was cornered into rejecting 2 Maccabees while debating John Eck on Purgatory. It has become standard now to mention Gary Michuta's argumentation on this from his book, Why Catholic Bibles Are Bigger for historical support on: Eck vs. Luther= remove 2 Maccabees.
That awful Luther just couldn't stand Roman doctrines, so he rejected all the Apocryphal books. But wait a minute... there are a few other Apocryphal books that go along with 2 Maccabees! I don't think I've ever heard a Roman Catholic explain which Roman Catholic doctrines the other books teach and why Luther rejected them.
The fact is, since about 2000 years or more (back then about 1500 years or more) there were two lists of canonic OT books.
It is certain one of them does NOT contain 2 Maccabees. It is somewhat disputed whether the other contains only 2 or even 3 or 4 Maccabees (Roman Catholic OT's end at 2 Macc, Roumanian Orthodox ones at 4 Macc, a k a Josif after Flavius Josephus, considered its author, a k a appendix to OT).
Now, it is also certain that Luther was not SUCH an unprincipled bungler that he would have stayed with the larger list while unilaterally rejecting one item in it. So, if he wanted to keep 2 Maccabees out, he had to stick with the shorter list.
One problem : up to then it was only Jews, rejecting Christ, who were known to have chosen the shorter one.
This was so in editions of Biblia Hebraica, but also so in the Hebrew text from which St Jerome translated the OT books (except certain ones, including 2 Maccabees) in the Vulgate.
Luther's solution was to fiddle with Patristics. St Jerome is known to have expressed a personal preference for including only the Hebrew books, not ones he had to go to LXX for. Hey presto, Luther had Patristic support! Or ... not. St Jerome did express this personal preference, but it should be noted that originally his Vulgate project was mainly there for debate with Jews, who back then used to point out where LXX diverged from their version. St Jerome's expressed preference COULD be read in the light of this purpose. However, even if he had a fleeting thought on 2 Maccabees not being divinely inspired, he did not stick to it, like Luther at Reformation, he rather obeyed the preference of all the bishops - expressed by his correspondent St Augustine.
So, even if no other "Apocryphon" had expressed (indirectly) Purgatory, or Indulgences, if Luther WAS to reject 2 Maccabees, which did so, he had to reject the rest.
In fact, the admonitions of Tobit also do express Indulgences.
The acts of the angel Raphael in Tobit would to many men around 1500 have looked like magic, superstition. And the book had encouraged considering St Raphael as one of the three archangels, with Gabriel and Michael.
In Daniel, chapter 3 is also "an addition" in so far as LXX and Vulgate and other RC versions are longer, including the song of praise of the three young men in the furnace.
Parts of that song would either qualify as "animism" or as "adressing angelic beings". Neither of which were high priorities on the Renaissance based, proto-"Enlightenment" and Humanist side of Reformation. Luther's mentor (who remained Catholic), Erasmus of Rotterdam, had lampooned "that sort of thing" in Epistulae Obscurorum Virirorum. Exactly as with how St Raphael made the exorcism and the healing of the eyes.
OTHER sects have had OTHER reasons to reject the seven books in question.
Judith (as well as a place in Judges) give parallels to "blessed art thou among women" in Luke. If we judge Luke by these two parallels, the angel was declaring the Blessed Virgin had won a major victory for Israel or defeated a major enemy of Israel. Since she had neither killed a man by a pole through his head like Sisera was killed, nor by cutting off his head, like Holophernes was killed, one can understand why She went "what do these words even mean" until they were repeated and she understood the parallel and gave a parallel song of praise - the Magnificat. She had never even once sinned, she had - even before becoming Mother of God - defeated the old serpent. I suppose there were already commentaries on Jael and Judith's victories saying how Holophernes and Sisera embody the serpent and were therefore struck in the head. If so, these would certainly have helped her to realise it was none less than the Devil she had defeated, since her fight was not against flesh and blood (see Ephesians 6:12).
If Luther did not mind this very Mariological implication of Judith, some modern "rejecters of Apocrypha" (which aren't such, the word means sth different and a different set of books, even for OT) very much DO mind this.
Baruch on the other hand, well, for some Renaissance men chapter 3 mentioning giants and God speaking to stars who answer might have been "too much", but to Jews about 1400 years before Luther, the thing which would have been "too much" was rather 3: This is our God, and there shall no other be accounted of in comparison of him.  He found out all the way of knowledge, and gave it to Jacob his servant, and to Israel his beloved.  Afterwards he was seen upon earth, and conversed with men.
Was seen upon Earth? Conversed with men?
Sounds like Jesus with the Apostles and with others, even if this does not quite fit the past tense. But the rabbis would have been very aware that such a description about events that in Baruch's day were past could also imply a prophecy about what in Baruch's day was still future. I e the days of Christ. I suppose this goes along with diverging interpretations of the three angels hosted by Abraham. To a Christian this could easily be a reference for Baruch 3:38, the Three Persons of the Blessed Trinity appearing like angels. To a Jew after rejecting Christ, such thoughts were a no no. The angels were JUST angels, JUST creatures. And if God indeed conversed with Job, Moses, Elijah, they did not see Him on earth.
That would be why Jews chose the shorter list of OT books, while Christians at least of Greek language choose the longer one, in the shape of the LXX. Not sure whether Peschitta has or lacks these books, I think it has them. Or thought. Checked, wrong. At least according to list on http://www.peshitta.org/. It ends - very much like Hebrew Bibles - with 2 Chronicles.
They had their reason, Luther had his, for Peschitta I think it was simply translated from the shorter version, so there was no active choice.
But there is a thing to note here. Even if Luther does reject 2 Maccabees as to divine inspiration, he does not reject its historicity. So, it is certain, historically speaking, even if it were not in the word of God, that a priest did sacrifice for purging dead people of their sins, and it is certain, historically speaking, even if this opinion were not in fact a doctrine in the word of God, that someone (whoever wrote 2 Maccabees) actually approved of this.
This means something like a doctrine of purgatory (some Greeks would prefer "retroactive efficacy of prayer") was around before Jesus came. This in turn means something if nowhere in the New Testament we see Jesus actively rejecting it. And it gives us a clue about the most probable reading of "salute the household of Onesiphoros".
Now we deal with the defense:
Contrary to Michuta's caricature of Luther pre-Leipzig, the reason why Luther could quote Sirach and Tobit is because Luther was heavily schooled with the Glossa ordinaria. When commenting on the apocryphal books, this work prefixes this introduction to them: Here begins the book of Tobit which is not in the canon; here begins the book of Judith which is not in the canon' and so forth for Ecclesiasticus, Wisdom, and Maccabees etc. The schooling Luther received informed his opinion on the canon. Even the Occamist influence in Luther's life would probably informed him similarly. Michuta himself notes Occam held to the allowance of reading the apocrypha, but that the books were not canonical (p. 218).
It wouldn't be odd to find Luther familiar with or fluent in the apocrypha, but that doesn't mean he believed it was canonical scripture.
I consider Luther fundamentally honest on this issue. He denied the authority of 2 Maccabees to establish doctrine because that was simply how he was trained as a theologian, and he followed a tradition which denied the Dueterocanincals authority to establish doctrine. Luther in fact provides detailed opinions of the Deuterocanonical books in his biblical prefaces. I see no reason to grant that his entire opinion suddenly shifted because of Eck at Leipzig. Luther quoted from the Deuterocanonicals throughout his entire career, in a manner consistent with the views expressed in his Biblical prefaces. Michuta's paradigm has no way to account for this.
Well, supposing Luther was himself that honest, at least he missed the point about Jesus not actively rejecting Purgatory or Indulgences, a doctrine PROVEN to have been around among Jews in his time.
And others were less honest. If Luther had been right, these would in the Lutheran community have been outweighed by the honest ones who were right for honest reasons - but since Luther was wrong, Lutheranism is not a "communio sanctorum" and there is no sharing of merits from better to worse Lutherans as there is with Catholics.
Hans Georg Lundahl
Immaculate Heart of
the Blessed Virgin Mary
* Quotes from : Beggars all ... : Why Luther Removed 2 Maccabees from the Bible
** Yes, they are open after vacation, again!