Why?
Oh, that's easy to answer.
Because the library datastore is the actual filesystem of the device, not a database.
Kobo stores its books in a database.
(See its reviews and forum for the downside of using a database as an ebook library.
)
Basically it comes down to performance: you can either use the filesystem as a datastore and have total control over how to organize your books or use a flatfile database that gives you some sorting and tagging but dumps all the books in the same location. Either will give decent performance. Try to run a full, flexible database and performance will tank. Plus the books will be hidden from the outside.
Guys, we're talking 533MHz ARM cellphone processors in these things; not GHz-class intel Core with a GPU on the side.