Generally speaking: sidenotes are excellent, footnotes are fine, endnotes are terrible. On the web, as a typically-not-paged medium, “footnotes” practically always actually means endnotes.
Do search around for other sidenote implementations, too. I like the markup and presentation I end up with, but you’ll also find other approaches to mobile support in particular, involving things like checkbox hacks to toggle visibility, or just flat-out requiring JavaScript.