While Cool Reader with its internal file manager is (still?) not available, a good thing would be to have "auto collections" something like the ones rupor implemented on T2: so that each folder with books automatically were shown as a separate collection or a shelf. You can have other shelves as well, those auto-shelves do not replace the regular ones.
That would eliminate the need to have a separate file manager.
As to the inefficiency of folders as the way of organizing books - maybe so, but with huge numbers of books it is a fast ant simple way. It does not require importing books into Calibre. Besides, it is not clear how many books Calibre can really handle before choking.
And in a case of multi-author series etc, I add "see there" instead of an actual book several times. It is really no big deal to get to the book. If you have a file manager, that is
.