I think it was stated by Barclay (Moriarty's keeper) in a book that the Moriarty cube had been destroyed in the destruction of the Enterprise-D. Immortal Coil, I think (where they also made an android with a holographic brain).
But that's easy enough to ret-con to bring Moriarty back for a novel about AI rights. I do think Star Trek has failed to adequately address the issue. (Unless there's something in Cold Equations, which I haven't read yet.)