Completely agree with you and David on these points:
(1) Almost nobody is coding popup footnotes to the Epub 3 spec in ebook source files (similar to the early days with HTML 'wild west' coding). For example, it's rare to see use of the epub:type attribute, the specified values of that attribute for note type content, and use of the <aside> tag.
(2) It is pretty much up to reader app developers to interpret how to render footnotes, endnotes, and other adjunct content. The processing requirements in the above spec doc are so wide-open, it seems like the sky's the limit. :-)

So I agree with all that, but whether ebooks are being coded to the spec is not my point in this particular thread. My focus here is really the desired user experience with footnotes. As I listed above, there some leading epub readers/apps that appear to use logic to infer the intent of a link, and render notes successfully as a popup (regardless whether the book's source code for linking is fully Epub 3 compliant). All of the apps I listed, they seem to be able to display the specific footnote content you clicked about 90% of the time, and when they fail for whatever reason (for instance, as with the Kobo example I gave), they fall back to navigating to where the note content is. Even Kobo handles this ok most of the time, but it especially chokes on books with a lot of end notes, and the others don't.

The 3 nicest implementations I've seen yet from a strictly user point of view are FB reader, Kindle, and KOReader. Also Calibre reader handles it well. KOReader just nails it, they render a single footnote quickly and smoothly, without excess page flashing and without needing multiple reloads (Kobo struggles badly with excess reloads, even when it successfully loads the popup). I have to wonder if maybe KOReader devs used a script to pre-load the related note content for each rendered page and dynamically render it when clicked. Kindle appears similar, with just a slightly longer delay and it appears to me, an extra page load. FB Reader has a beautiful implementation UI-wise. It's quick, attractive, and non-intrusive on the reading experience. It even allows you to customize in user settings some of the details about how the footnote is handled, styling, etc.

So I guess my takeaway point is I hope we can convince Kobo to improve the note handling (in my subjective opinion of what is the 'desirable behavior') similar to the other apps listed. I think a lot of readers would find that note-handling behavior desirable; the fact that the other readers are doing it is one evidence for that.