There's centuries of research in organizing a physical library, and some reasonable if contentious schemes.
Organizing your ebooks, whether epub, pdf, text, reaction gifs, whatever, can be much more ad-hoc, and is poorly researched at all.
For reading, on Mac I use Murasaki for reading epub, it's scroll-based instead of page-based, but it's very nice; for PDF either Mac's Preview, or Skim which is especially useful for research, I often Merge Windows and have 5-10 books open in tabs in it. On iPad, I use Readdle Documents mostly, but it doesn't handle comics so those I open in Chunky Comic Reader, syncing over DropBox or iCloud.
On Mac, as long as Spotlight works, it kinda doesn't matter how the folders are laid out, but it might take hours or days for new things to fully index. If Spotlight stops working, mdutil -a -E will erase existing indices and start over. I dunno what you do on medieval filesystems without xattr, but I don't think non-Mac users can read anyway.
If I refer to a book by terms not in title or obvious search index, I put those in the comment or tags (select file, ⌘I for Info). I use color tags for all media: Green = to-read, Red = error/editing, Yellow = important, Gray = read. I also have an Automator action to Label Gray & Open, mapped to ^⌘O, which I use when working thru a series.
For all my ebooks, I just have a big Books folder in Dropbox that I subdivide by category. Mostly I rename book files Lastname,Firstname-Title-Year.
ls:
!inbox/ Algorithms/ BASIC/ Business/ C/ Calibre/ Classics/ Clojure/ Computer Theory/ Design Patterns/ Elixir/ Game Design/ Grimoires/ Groovy/ Haskell/ HauntedMansion/ Hewlett-Packard/ History,Rome/ Horror/ Humor/ Hypercard/ Interzone/ Java/ JavaScript/ Jazz Age Pulps/ Julia/ Literature/ Logo/ Mac/ Mathematics/ Mondo2000/ Mystery/ NetRexx/ Non-Fiction/ Obsolete/ OMNI/ Pascal/ Phone/ Pilot/ Python/ RasPi/ Retrocomputing/ REXX/ Scala/ Scheme/ Science/ Science Fiction & Fantasy/ Technical/ UFO/ Unfiled/ unix_cd/ Vim/ Virtual Reality/ Web/ WIRED/
Which I'm pretty sure will make a proper librarian swear at me, but it's shelving what's important to me.
Books is currently 173.82 GB for 193,214 items. That doesn't count Comics, Gamefaqs (by which I mean all videogame texts, not just faqs), or RPG, where my X,000 game books are.