If you're using footnotes to cite things, you're doing it wrong: inline citations exist. If that's not enough for you, use a different syntax (say, ^[1] instead of ^1). If you're using it to define terms, you're doing it wrong: use a margin note. If that's not enough, you should probably typeset a nice box that makes definitions easy to identify. Footnotes (imo, of course) should only be used as a "here's more information for the curious" and should similarly only appear at the actual foot of a page (I despise endnotes).
My experience is biased towards print and print-like (PDF) use of footnotes, but I don't think it's much of a problem to expect users to click every footnote when provided with a convenient pop-up UI like in the OP, provided that you've clearly defined a convention or pattern of their usage to your readers.
I do wish websites showed footnotes on hover, though... jumping within the page is nonsense and often mucks with URL sharing.