Which is bad if them notes are not ornaments only. So there should be some fallback. I guess a good approach would be to collect the content from some p.marginnote elements which would be hidden if JS is present and left intact if not. So, like
<a href='#' mnref='gcc'>GCC</a>
...
<p class='marginnote' mnname='gcc'>The GNU Compiler Collection</p>
With JS, they'd become margin notes, whithout it, they'd render as plain footnotes.