Xournal++ is old, but it can directly write on PDFs with both pen tablet and scanned image insertion, and can probably add/remove/reorder pages too— Technically I think its file format links to/embeds the whole PDF file, and then probably exports a new one with stuff added on top, or something like that, but the end result is usually that you can directly edit the PDF.

Or do you mean some kind of cryptographic signing? Well, it looks like Adobe offers a webtool too?