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Yep, that's my mean reason to use the Calibre Kobo TouchExtended driver.
For standard epubs the Adobe Digital Editions renderer is used, and as you found out (as did I) it handles footnotes very badly; I succeeded in getting to the note exactly once, instead of getting the normal touch screen action. For Kobo epubs they use the ACCESS renderer, which does it very nicely with a preview popup without fail.
As I read lots of non-fiction (which tends to use footnotes extensively), I switched to kepubs (a conversion which the TouchExtended driver can do on the fly when sending ebooks to the device if you want it to).
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Ahh thanks, I wasn't aware of the TouchExtended driver, will try it when I get home.
Still hope they'll fix the footnotes on ordinary epubs though