Personally I would like to see an option in the admin panel that lets us add our affiliate ID to the copyright footer, but still keep the same anchor text etc, if that makes any sence?

You don't even need affiliate ID. Just verify your domain, and if the referring URL is from your domain then boom affiliate :P

I don't know if this feature was implemented yet.

We are going to work on a way, in a future version of IP.Board, for the affiliate ID to be encoded in the link we put in the footer. That way you get credit there too. We're nice like that :)