Sioyek currently does have a bookmark support which is external to the PDF (you can bookmark locations in PDF file and you can later quickly search in those bookmarks).
But I assume you mean some sort of visual annotation that is drawn on top of the PDF?
No typing, just selecting a few words or lines. It's all collected in a notes page/doc, you later look at that and hopefully see or remember what was wrong and fix the original.
Limited, but helpful.
Sometimes I "translate" a difficult passage to something I can understand (on paper I might write this in margins). At other times, I end up accumulating definitions of terms (or letters) while reading a paper. Today I write those on a separate piece of paper so I can have my definitions table viewable at all times. It would be really nice to have that sort of thing stored and available while I'm working my way through a paper (perhaps similar to the portal feature).
I mean things like Okular has: highlighting text (like with a yellow highlighter on paper books), freeform draw tool (like scribbling with a pen), adding short text comments and longer notes, etc.
To illustrate, the annotations in an old Okular version looked like this: https://docs.kde.org/stable5/en/okular/okular/annotations.ht... (the yellow note box, the green lines and so on).
There's a small picture at https://okular.kde.org/ too, it shows a newer version.
DISCLAIMER: Not saying that Okular is THE reference to follow, I'm pointing it out because I've experience with it, and for example their decision to save annotations into the PDF itself is in my opinion a lousy one. But the idea that one can free-form annotate and add even longer comments to the pages is a great one. The annotations are like scribblings in a book margin, very useful both when studying and when referring [ * ]. And this is something Okular has done much better than e.g. Evince.
[ * ] Of course, one could use a more elaborate tool to keep references, notes and quotes etc., like Zotero.
Edit: typofix
When it comes to my notes, what I read, or when I read it, any kind of cloud component or connection to the internet is a showstopper for me.
> sync hypothesis <-> zotero
Not sure what is the good presentation for it: clicking or hovering, overlaying or pop-up or a separate window... I suppose to figure the best UX is not trivial, but even mediocre UX would be really great.
And as others say, ideally keep the annotations outside of the document itself.
I find the drawing UX of Okular very lacking - if this application could have a simple, clean annotations interface that produces clean lines with a tablet, this would be huge for me.