My guess is that Apple was looking for the least expensive way to sync them, so they treat them as emails, and let the IMAP protocol keep them in sync.
That way they didn't have to develop their own sync system, as well as write a new "Notes" portion of www.me.com (because you know peoples' heads would explode if they couldn't see their Notes when they use a browser to logon to me.com). 🙂