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I have two thoughts on this. One, hyperlinks would be an acceptable way to deal with footnotes (essentially making them endnotes). The current problem is that of the few readers that presently support epub, DE has no way to return from a hyperlink jump, rendering the method useless. Since DE is the big gorilla right now, this is a major problem.
My second thought is that other means of dealing with out-of-context information like footnotes and definitions can be more useful and less disruptive to the reading process. In particular, I'm thinking about popups, but other methods may be suitable. The problem with popups is that some of the properties required to make them work are not mandated by the epub spec. You can use them, but there is no guarantee that they will work on any given reader. As I have mentioned before, DE doesn't work with popups.
I think these issues need to be addressed, both in current reader software and in future versions of the epub spec.
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