I’ve run into exactly the same issue with my large ttrpg ebook/pdf collection (+100k file data hoarding… it’s not a problem, I swear) and I’ve not really found a good option I’m entirely happy with. Calibre duplicates everything and I don’t like the thought of having my collection’s organization tied to a specific piece of software if I just delete my duplicates. Plus I’m elitist and think the UI/logo are gross to look at.
Zotero is the least worst option I’ve found, but it’s geared towards scholarly journals and such, so not great, but serviceable. Not sure if it’s on linux though.
Jellyfin is apparently able to handle ebooks with a plugin, though I didn’t particularly care for it when I tried it months ago.
There’s a handful of other ebook software out there, mostly geared towards comics/manga, so depending on what you have those might be worth looking for.
I’d like to use Obsidian for it and just turn the directory into a vault and let it automatically scan the folders for files, but that doesn’t work great either.
The best piece of software I’ve seen that could potentially handle it is an app called Stashapp… which is unfortunately geared towards adult film. But it’s feature-set if it could be applied to PDFs seems like it would be ideal.