I doubt nintendo is upset that they use friendscodes, its probably more the fact they used www.friendcodes.com something they feel entitled to own because they have the patent on the phrase. If anything i would sell it to Nintendo they themself would probably never use the domaine but whatever. Then take all that big cash setup a new exchange site and be done with it.
Honestly Nintendo doesnt have the right to a domaine just because they hold the trademark for the word. Internet Domains have always been first come first serve. At worst they could force them to take away refferences to Nintendo's friends codes but thats it. Even then its not soemthing that would be eaisly won in court. Specailly when they are telling a fan site to take it down not a competitior.