Yeah, I also work with Latex, so this is very helpful, thanks. (Although I usually don’t try to do the whole thing from Scrivener).
Links definitely help in case of endnotes, although I still don’t like when I have to actively interact with the page I’m reading (by clicking a link instead of just glancing down at the bottom of the page). But this is really just personal preference, and page aesthetics may be more important for some. (There is no, absolutely no excuse however for digital books with endnotes without links. That’s the one that really drives me crazy when I read, so I just stop looking at the notes altogether.)
This is tangential, but it also seems to me that the academic style is changing. There are a few very good academic journals in my field that strongly discourage footnotes, and consider it bad academic style. And while some friends of mine have managed to convince OUP to use footnotes instead of endnotes in their book, some didn’t.