Thanks for your detailed answer.
Sounds like it totally makes sense to keep it that way. Sad that kobo doesn't makes it more easy to integrate third party reading apps for specific mimetypes.
A script launched when the storage is unmounted could maybe add the needed paths to the database, making it possible to parse that list from the db, avoiding the need to walk the whole directory tree at boot. But anyway relying on inotify for too many files seems problematic, there's probably no way this could scale to more than a few books without big downsides...
Edit: not related to KFM but wouldn't it be possible to trick nickel replacing the original pdf reader with a wrapper that would start koreader? Might be totally stupid, I need to find a kobo on which to experiment stuff and understand better how nickel works.