The Great Library will probably not be reduced in size because...well...it's Great! See also: massive, immense, superlative, etc. It's probably actually several times larger than what is represented in game, but the sense of size is kind of important.
As for the rest, yeah, it's been something of a standing issue with the books and their removal between people taking them and the normal behavior of the clean-up script. They also sorely need to be updated for lore accuracy. So yeah, it's been one of those things that comes up in my mind now and again, but the priority has always been low.
Anyway, just framing the topic a little. Thanks for the suggestion!