Hi,
just my 2 cents: This is a usability thing and tapping on Screen may end up in several actions deending if you were able to hit the hot spot. If you miss it even by only 1 Pixel you may mark some text or going back or forward one page or whatever depending on the reader you are using.
Personally i don't like numbers only and the wurst thin is to put in into a <sup> element...
But maybe its possible to enhance the plugin by some kind of a template like
to get an individual link to the (foot)note? As you can see, i personally do not only have brackets around it, but an arrow as well. That makes the link "clickable" for my fingers
|\/|aui