Let's take a close look at
http://www.wcaao.com/
- It is a website
- Its name is "Wing Commander: Against All Odds RPG"
Therefore, there's nothing wrong with a fan nominating "Wing Commander: Against All Odds RPG" as best WC website of the year.
The fact that it was nominated doesn't mean there's been a terrible confusion by a fan who actually wanted to nominate something *else* which is now called a different name and hosted by a server that is now called the other thing-which-is-not-a-website's previous name (or whatever nonsense you care to come up with)... the fact that it was nominated means that it was nominated, and that the other thing that now goes by another name, or whatever your point is, wasn't.
The people organizing a fan-nominated voting shouldn't really care if one of the nominated sites isn't an actual RPG anymore or whatever you're trying to tell people. The fact is that there is still a WCAAO website online, which claims to be a WC RPG, and as such it's still liable to be nominated by someone.
If some of your fans don't even know what to nominate, you should spend your time trying to do a better job at mantaining whatever "it" is instead of asking for nominations to be removed.