This doesn't really address the core issue, but it might help some, particularly with non-Connect texts (that is, from somewhere else).
I noticed that the PC's hard drives show up in Connect. I played with that a bit and I think I'm going to put my personal files in sorted directories on one of the hard drives and pull them from there directly to the Reader when I want to use them (without putting them in the Library at all). I'm finding that I don't really want much more than a half-dozen books at one time on the actual Reader, so I think it has potential for my needs, anyway.
When you look at the files on the Hard drive through Connect, all it shows is the actual file name (no meta-data), but that's managable, I've been dealing with it for years, so I already have a system that works for me.
I also played with renaming the encrypted stuff and shifting it around, and it too seems to work fine with this approach, but you're right that it's a pain to manage, melchioe. I think if I start it now while I still only have a few of them, I'll probably be okay.
Perhaps I'll store the files on R/W CD's, then I'll still have something to put on my shelves.