Wikipedia combines both in a way thats quite alright I think.
On wide screens it uses the regular links. On small screens they still have the footnote section at the bottom but when you click on the link to a footnote it actually shows a special pop over box that takes up no more than half of the screen. If it is too large it will be scrollable.
I think this way is sufficient. If wikipedia implements it this way mobile users will probably also expect the same behavior. We can however style the links to be a bit larger somehow to make it easier to click on them.