The epub2 shouldn't be a problem. From what I've read, I believe that as long as the footnotes have their "there and back again" ids and hrefs, and the actual footnote text is less than 5,000 characters long, then the reader should be smart enough to pop up the footnote windows.
EDIT:
Here are the actual popup requirements from that Kobo page jackie_w referenced:
Quote:
The link references a location in the EPUB and also references a specific node within the HTML. Ex.
<a href=“chapter.html#uniqueID”>link text</a>
Where chapter.html is a file within this EPUB and where uniqueID is the id of a node within that html document.
The content in the node is nine characters or more once stripped of the HTML tags. Ex.
<p id="uniqueID">123456789</p>
The node being linked to is less than or equal to 5000 characters.
The location being linked to comes after the location being linked from. Ex. A reference in Chapter 2 links to a location at the end of the file titled Endnotes or a reference at the beginning of Chapter 2 links to a location at the end of Chapter 2.
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/EDIT:
The epub:type attributes are just supposed to make things more sure.
If the popup doesn't happen, you should theoretically be able to just follow the links both ways. But, as you've found out, footnotes on Kobos don't always seem to do what they're supposed to do.