Maybe I'm old school, but I don't understand the concept of a "library". I have directories on my filesystem(s), files in those directories, and amazingly powerful applications to navigate them (Total Commander / mc / Krusader). Why would an ebook reader even try to do the navigation for me? It should display an ebook, and I'll take care of the rest. If it's showing me the file system, it's redundant. If it's showing…
You're right that this often causes problems. Anybody who has tried to salvage an iTunes library can attest to that.
However you're downplaying the positives to having a metadata database, and you're also ignoring the teeming masses who don't care about the layout of the file system as long as it's displayed in the app.