[jackie_w]

Calibre's Check Book tool shows display:hidden as an error, perhaps it appeared in a later version of CSS than is typically supported by ADE-style renderers on eink devices, such Kobo's renderer for standard epubs.

I must admit I don't use any special CSS or markup for footnotes, I just use simple anchors which seem to work as expected on the Kobo, i.e.
- kepub: choice of pop-up or link-to-endnotes page
- epub: link-to-endnotes page only

They work no matter whether the book is epub/kepub and no matter whether the kepub was created from an EPUB2 or an EPUB3. For example:

Chapter HTML file:

<p>... a rule instituted hundreds of years ago to prevent this branch of the Church becoming too big for its boots.<sup><a id="back02" href="endnotes.xhtml#fn02">[2]</a></sup> But ...</p>

Endnotes HTML file:

<p class="footnote"><a id="fn02" href="chapter1.xhtml#back02">[2]</a><br/>Which were of the one-size-fits-all, tighten-the-screws variety.</p>

CSS is very simple:

.footnote {
    margin: 0 0 0 2em;
    padding-top: 3em;
    text-indent: -1em;
}
sup {
    font-size: 0.9em;
    line-height: 0;
    vertical-align: super;
}

ETA: I'm not saying that the above is the best way or the right way of doing footnotes, just that it is a way which seems to work trouble-free on a Kobo.