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I don't think the epub specification would have to add anything particularly exotic to support pop-ups: just expand the amount of CSS covered to include :hover and related stuff. You can Google how to use pseudo-classes to produce pop-up footnotes in a web page, but I don't know of any reader that supports this.
And, if I can bang my favorite drum just a little more, epub will have to include support for footnotes and other things if it is ever going to be suitable for textbooks and scholarly publications--a big market just waiting to be addressed.
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