Twitter messages are limited to 140 bytes (not characters, if you are multi-byte speaker!). However, a lot of messages now carry the usernames, either for @replies or for simply refering to @user in the message. As the twitter userbase grows, people would start running out of shorter names like @t, @ev or @1ndus and eventually go the email route email@example.com.
The day is not far when twitter screen names would @mylongname2008. This one takes 10% of the text from 140 available.
At the minimal twitter should count out the @replies and @user from the 140 characters and make that part of the meta-data.
The API can handle this transparently, It just requires adding a new field called to-user-screen-name in the API. The API already has all the information for the sender ids, sender screen names, reply-to-user-id, user-id, etc.