Having [someurl] turn automatically into [1] is an elegant solution. The heedless coder leaves a clean external link behind, not a godawful URL, which might be two lines long and rife with % signs, and the careful coder has a choice of simple footnote or prettified link.
Yeah, that's a pretty good argument.
How about this:
[http://www...] renders (a href="http://www...%22)%5B1%5D(/a) with autonumbering, [http://www...%7Ctext] renders (a href="http://www...") text(/a) (the pipe can optionally be a space), and [http://www...%7C] (note trailing pipe) expands to [http://www...%7Cwww...] ?