Seems to me like this only confuses, since conversations are separated by address/phone number. Are their any advantages, or is it safe to remove all email address from my iMessage?
In the past, the main reason to iMessage to emails, was so that users could receive them on their Mac, iPad, or iPod Touch. However, iOS 6 and Mountain Lion allow the user to sync Messages across all their devices. This works great as long as the recipient has a iPhone, and have updated their software to the latest version. If they just have an iPad, for example, you would want to text their email address, as they wouldn't have a phone number to associate with. Also, some people don't update their devices as soon as one comes available, and as a result, some may still be using iOS 5 which wouldn't support that functionality.
Beyond those reasons, there should be no reason, why not to text someone's phone number. In fact, that is basically all I do.