Update: nowadays, in Safari 5.1 on OS X 10.6, all keys seem to work for both Ctrl and Command, including Command-B and Command-I. I guess an update on Safari has fixed this; on an OS X 10.5 Safari 5.0.5 still showed the old behaviour, but not after I now updated it to 5.0.6.
Oddly enough, in Safari: Command-L does work (a tiny bit annoying, as I'm used to that to go into the location bar, but that's not happening a lot when I've started typing something). And so do Command-Q and Command-H (more annoying, as those are Quit and Hide on a Mac). Also: Command-G, Command-K, Command-O and others.
But, in Safari:
not so much for bold and italic.
So: maybe Safari is only listening to keys that normally have some other meaning, and ignoring anything that Safari does not know about? If true, then map Command-B and Command-I to some of Safari's menu items, and you're settled.