First, Haml doesn't support includes (at least not in our setup), so you have to use the Slim templates instead. (A better choice in my mind anyway).
However, at the moment, Slim is only configured to resolve an included file relative to the file that's including it. Instead, I would expect Slim to search in all the specified template directories (in reverse order, just like it does for the main templates).
As it turns out, I found a note to myself to report this problem, so I went ahead and filed an issue for it.
One this is resolved, you'll be able to put _footnotes.html.slim in template-overrides/html5 and call Asciidoctor as follows to use it:
$ asciidoctor -T asciidoctor-backends/slim/html5 -T template-overrides/html5 input.adoc
It's necessary to use the Slim templates as a base since the footnotes are not handled as a separate node (like the outline)*. However, be aware that the Slim templates have drifted slightly from the built-in html5 converter and are in need of being updated.
Cheers,
-Dan
* I think a strong case could be made for updating core to handle the footnotes block as a separate node. This would be similar to what we do for the outline (i.e., TOC content).