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xournalpp
Xournal++ is a handwriting notetaking software with PDF annotation support. Written in C++ with GTK3, supporting Linux (e.g. Ubuntu, Debian, Arch, SUSE), macOS and Windows 10. Supports pen input from devices such as Wacom Tablets.
There is pdjam which might be a part of what you are looking for.
For OCR there is tesseract.
xournalpp would be my first suggestion; this is what I typically use when I want to add a facsimile of my physical signature.
For a lightweight epub viewer, I'd probably go with mupdf or zathura. (Till recently I'd have said llpp which is based on the same codebase, but I think the developer has removed the sources for reasons having to do with the war in Ukraine.) However, I think these are based on the same library as Sumatra for Windows, so you may have the same problem.