Apple’s support for ePub 3 footnotes is detailed here by Liz Castro.
In short, if the footnote link has the epub:tupe="noteref" format:
<a epub:type="noteref" href="#n1">1</a>
And the footnote text sits in an <aside> tag with the epub:type="footnote" format:
<aside epub:type="footnote" id="n1">
<p>This is the footnote text. However, if I <a href="http://stackoverflow.com">click this link</a> it does not work.</p>
</aside>
Then you get neat pop-up footnotes on iBooks.
Links in footnotes (as I’ve shown here), however, don’t work. When you tap the link the popover collapses:
Any ideas on what I need to do to get this to work? Am I missing an epub type declaration somewhere? Or is it just a bug in the iBooks popover implementation?
[NB: my current workaround is to have the footnote in a at the end of the chapter—so as a normal endnote—with the same epub:type="footnote" tag. This means that it will always show up there (unlike the <aside> tag, which is hidden) and you can follow the link at the end of the chapter, but you still get the in-place popover for information in the flow of the text.]
Same problem here, I made the conclusion that this is a limitation in iBooks popover implementation. Playing with the @_target attribute has no effects too.
Until Apple fixes it, I’d recommend to use non-linear documents for notes with complex content (and to no include them in the ‘nav’ table of content). In an automated XML process, this can be pretty easy to setup and is effective : when the user click on the note reference, a new window will open with the complex content (links by example). The user can close this window with the “OK” button on the top right of the screen.