What I have seen done that works is instead of using a single character superscripted to make it even harder to press is to use thinks like...
Go to the footnote for this sentence. This is the next footnote.
That way, it will be easy to hit the right spots on the screen.
Now, as for the font size being a reason why the links do not work properly is rubbish. Either they are not codded correctly or this is yet another Kobo bug. Given that they work everyplace but a Kobo Reader, I would say it is a bug in the Kobo.