I am currently reading a book with many footnotes (endnotes) as well.
It works quite okay for me but that's because my Calibre is set up to filter pretty much all CSS styles, so what I have is actually something
2 instead of something
². So even though the endnote links are just numbers I still have a good chance of hitting em in no more than 3 tries
I should mention though that I'm reading with a "comfortable" font size, the smaller you make it the harder it is to hit.
Seriously though, I only half blame Kobo for this, the entire endnote concept is utter nonsense, hope it will work better for EPUB3.