Yep, as an ebook "designer" for several academic authors, I can categorically state that even in fiction, they loves them footnotes.
Now, in an ebook they are actually "endnotes" (which is usually the case anyway in academic papers) but... we can link to them directly where ever they are stored physically.
But what about the link back? The usual way I've been doing it is that the ID= of the <a..> tag of a footnote reference in the text takes you back (via the <a target=...> tag of the footnote itself to where the footnote was jumped FROM. On many readers, that means that the line containing the footnote becomes the top line of the screen.
But, sometimes it's better to place the ID="..." in the PARAGRAPH TAG before the actual footnote reference in the text rather than in the <a.../a> tag itself. That way, the back-reference takes the reader to someplace that provides context for the footnote.
Oh, and @Hitch: I HATE footnotes! (I'm lazy...)