I'm using Mendeley to read and annotate papers, and Evernote to organize my notes (and screenshots of figures, etc) about them. Either syncs between my laptop and phone, guess it would be the same for a tablet.
I also use my phone as a makeshift scanner for handwritten stuff, just photograph and put the photos in notes with a short typed summary so I can search it later. I do this for annotations from conferences and workshops.
In Evernote, you can link to other notes in a hyperlink-like format, which is quite useful when making summaries and pulling together ideas.
That said, I'm sure that Google docs, OneNote and (if you want to self-host and care about open-source) Nextcloud notes can do much of the same.
Just a suggestion: If you're already using Nextcloud, why don't you try Nexcloud Note? There's also an Android App for it which is pretty great. Except if you're on iOS, then you might be out of luck.
AFAIK notes via CalDAV/CardDAV is not supported in Nextcloud (but I can't find the issue to it right now, sorry), so you'll have to use a separate App.
Personally, I recommend Nextcloud Notes which integrate very well into the system and also supports Markdown. You'll get a "Notes" folder in your user's directory where all the notes are stored and there's also a great Android App for it (and also an App for iOS, but I haven't tried that one yet due to the lack of apple devices in my home).
I don't know about any application for the desktop, though. Since everything's just a file, I open all my notes via my preferred text editor.
So I have tried just about every note-taking application you can self host, and I ended up just using text documents, markdown, and SyncThing. When I want to "share" a note, I just email the current version of that file to someone. This system is extremely robust and nearly never fails me. The best part is you don't even need a home server, though I think it is wise to set up a raspberry pi so there is always a sync target available. This will reduce the number of file collisions you have to resolve.
That all said, NextCloud Notes meets all of your requirements.
Remember that you don't actually have to use the NextCloud Notes app to access your NextCloud Notes files. Its just markdown, so you should be able to sync the files to android and linux devices, then edit them with a text editor.
I've been toying with the official Notes "app". My main issue is it doesn't work with the Android app, so I can only read the notes through the file explorer view.
How does Carnet compare?