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I also want to add one consideration:
Calibre uses the folders' structure as his database, which (probably, I'm not sure) is what allows two Calibre installation (for example in a dual-booting Windows/Linux PC) to share the same library. If you make a change (add a book, edit a title, change author...), it is reflected in the folders' and files' structure, so when you boot into the other OS and re-open Calibre you'll see the change "ported" to the other installation immediately.
If Calibre were to change the way it works, for example by using some sort of database interface to index and tag its files and to keep its metadata organized, it would (again, probably, since I haven't yet looked deep enough into its code) lose this nifty feature, because any change made to your ebooks, say, while using Calibre in Windows would cause data corruptions and disalignment once you open Calibre in Linux.
So, it would (probably) lose a feature that many like me love, to add a feature that a few others like you want.
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