The problem is the size of the link. In a paper book, having a little superscript number to indicate the footnote is OK. But, if you just wrap that number with tags to link elsewhere, you have this tiny spot on the screen to press to trigger the link. The kepub reader app handles this making the link larger. The epub reader doesn't do this. The only thing to do is make the link larger. Increasing the font size works but is probably not practical. I tend to edit the epub and change the footnote link to cover the word or phrase the footnote refers to. Or I convert to kepub.
If you don't want to manually convert the books to kepub, you can use the KoboTouchExtended driver in calibre. It will convert the books on the fly during the send. But, it doesn't save a copy of the kepub in the calibre library.
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