Hotmail works perfectly well in Firefox (as an aside, I recommend that you go to the Mozilla updates site and install an extension called "Hotmail Tabs" which lets you use the tabbed browsing feature with Hotmail). Automatic updates should still work OK too. I haven't a clue about MSN Messenger as I've never used it.
Messenger is a standalone program that doesn't need a browser to work. However, if you click a link in messenger, I think it fires up IE even if all your default settings are changed to Firefox. I'd have to check this at home though as I don't have Messenger here at work.