I do know that O'Sensei has been described as a prolific reader (hence my avatar), and I remember being told by someone (frankly, I don't remember by whom) that the bulk of his library was retained, along with most of his writings, by the family. I do think that Saito Morihiro ended up with some pieces, though. I suspect that Saito Hitohiro could shed some light on the whereabouts of that portion.
A lot of Osensei's old books are still in the dojo in a room in the extended section where he and his wife slept. Luckily the Great Tohoku Earthquake didn't do too much structural damage to this "newer" section which was completed in 1968 - about a year before he passed away.
Also David Alexander Sensei wrote this about staying in the dojo:
We stayed for several days in Iwama, and slept in O-Sensei's old storeroom next to the dojo (which was subsequently demolished to build the current "red room"). It was a very interesting place, filled with books and old charts of Kotodama symbols that O-Sensei used in his lectures.