Hyperlinks change the game. They make the difference between foot- and end-note largely irrelevant. Until such time as those hyperlinks pop-up a "window" above/beneath the referenced text, they (hyperlinked notes) remain—in my opinion—the most unobtrusive method of including ancillary or anecdotal information in ebooks.
The "bottom of the page" is gone, for all practical purposes. Reflow took it away. We traded it for the ability to choose any font and/or text size our little hearts desire. Any notational method that attempts to shoehorn the extra information into the normal narrative flow of the text is obtrusive, in my opinion, and therefore unacceptable.
If hyperlinks would have somehow been available to typesetters 100s of years ago, we wouldn't be having this debate today. There would simply be no such thing as a "foot"note. Effort was the main difference in the physical medium. Less effort for foot-notes ... considerable effort for end-notes. Hyperlinks have equalized that difference in effort. And for the most part, minimized it.
Keep in mind that even in the physical, typesetting world of books, readers were still able to to make up their own minds about how/when—or even if—footnotes interrupted their reading. A reader who just wasn't interested could read a book chock full of footnotes and never stop to look at one of them if they didn't care to. I say give E-readers the same latitude as P-readers. Stop trying to micromanage the reader's experience and just slap a link in there for those who are interested. They'll figure out what to do with it.
Last edited by DiapDealer; 11-28-2012 at 04:38 PM.