I have a large collection (it's 1000+ articles, pdfs, photos, notes, etc) of mostly "research" for several fiction books I'm writing as a hobby and also random ideas and DIY inspiration, etc. and although nothing has solved it yet and my use case is slightly different, I keep seeing people mention Evernote and similar programs, and I doubt it will work for your use case. I have tried:
- Evernote - It's been a while, but at the time it had no highlighting. Formatting text was also a bit of a pain. Attaching large files was a problem because of free limits (I didn't care about sync but you need it for clipping). But the biggest problem was organization. The notebooks were not enough and it was really slow having everything in one account. Tags did not really help the organization problem either because what I really needed were custom fields. Search was slow and it was hard to be precise because there's no custom fields to be precise about. Additionally for any actual writing, there's no note history on the free plan.
- Most of the Evernote alternatives - Although I didn't move my collection to them, I did try every alternative I could find. If there's any in specific you're considering, I have probably tried it. The problem with most is they were either too simple, buggy, old/unmaintained, or just plain Evernote clones, which already wasn't working. Also many good ones that might have worked were subscription only because they were cloud solutions with sync. Then some sounded promising on paper (wiki-like alternatives), but they would just make me waste time linking and weren't really what I needed. Also many use only tree organization which just does not work for me. Or they don't support attachments well. TagSpaces looked really promising for an on-disk solution but didn't cope well with moved files when I tried it.
- Scrivener - This is what I ended up moving to. It's not the most intuitive piece of software. Development, especially for the Windows version is incredibly slow. It used to not have sync, now it sort of does, but it's not like Evernote (no clipping). I don't really care for sync though, also I like that it was a buy once sort of thing. Now it's still pretty slow with search (made worse by the fact it sort of freezes instead of showing some loader), but I can divide what used to be my main Evernote notebooks into completely separate projects. You can also have custom "views" (lists of notes) which helps reduce a lot of searching. You can also easily search just one specific field although I do kind of miss Evernote's query language. What really sold me though was you can have a completely custom organization scheme. You can add different types of labels/tags, you can change the note icon, you can color code notes, but best of all you can set custom fields (it's like a really fancy database really). You can link to other notes. You can have a custom note card summary for the cards view. There's several different view types (list, same tree-depth together, note, card/corkboard). It was designed for writers, so it's easy to write in and keep everything in the same format, etc (all copied articles are nicely formatted about the same). You can take as many history snapshots as you like. Best of all you can have huge attachments. I have videos, pdfs, etc (known image formats and pdfs, you can see inside the program, videos, and unknown files open externally). You can also set a custom theme and shortcuts which was also really important for me (Evernote still doesn't have a dark mode!). Also although the on disk project structure is not exactly easy to navigate, it exists (i.e. attachments just get copied to a folder in the project, all notes are plain .rtf files) so you can use Drive/Dropbox to sync to other computers or edit notes externally.
I'm working on my own custom solution now, but Scrivener has worked the best for me for notes, articles, and "clippings" if you have a lot of that. I would not used it though for ebooks, or movies. Ebooks I use Calibre because it also has the tools to edit them, though you could have ebooks in Scrivener if you want, and Calibre as the reader. Movies I have only a few, and just use a folder. For quick notes I use Google Keep or Simplenotes. Then every once in a while will clean them and extract the good ideas to Scrivener.