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As far as I know Kobos can't be organised via the file system. Although you can store your books in whatever directories you like, the whole disk will be scanned. Organisation is via Shelves based on metadata inside each epub rather than file path. If you use Calibre to organise your books on the PC then it is easy to automate the set up of the Shelves as you wish e.g. by Author, by Genre, by Series (or combination of same). However I suspect you will be struggling with 20,000+ books.
I also still own an old Pocketbook, but it is the only reader I've owned which could use nested file directories for organisation as a standard feature. It was also possible on the older Sonys but only via 3rd party custom firmware.
As far as I know none of the current models from the other 'big name' readers, Kindle, Sony, Nook organise via the file system.
P.S. Calibre also has an add-on plugin specially for Fan Fiction, in case you're interested at some point.