It seems from your description (I don't have a kobo device) that one of the footnote links issues is that the link could be too small. A single "1" on a small screen (especially with small font) would be hard for the device to detect a touch.
Why not make the hyperlink a little larger - include more of the surrounding text. Unless there are two adjacent links that should not be a problem.
e.g.
instead of:
<p>This is a test link[<a href="..." id="link1">1</a>]</p>
you could use:
<p>This is a test link<a href="..." id="link1">[1]</a></p>
or even:
<p>This is a test <a href="..." id="link1">link[1]</a></p>
The only downside I could see is that link[1] would all be formatted as a link (ie. blue, underlined). I personally don't like links formatted like that - I remove all formatting and assume that the reader will intuit that it's a link based on it's content - but that's me. If you want just the numeral formatted that could easily be fixed with css and a span:
a {color:inherit;text-decoration:none;}
a span {color:blue; text-decoration:underline}
<p>This is a test <a href="..." id="link1">link[<span>1</span>]</a></p>
Cheers!