I guess because I learnt about such ciphers when our primary school only just got it's first computer, running at 4MHz, the conflation of webfonts and subst. ciphers never struck me before.

Before today I've seen this done with javascript and, TBH, I think that would have been the first method that sprung to mind but I've not really ever bothered to think about it.

Quick search only found one other example of this technique: http://eligrey.com/blog/post/tag/rot13 (rot13 fonts, lol) as well as this http://jsfiddle.net/QQ9WQ/ from the current author. It's hard to search as there is a font called "cipher font", which of course is available as a webfont! Of course there are lots of pages using js, like http://rumkin.com/tools/cipher/substitution.php which does some funky substitutions.