You could still put "Hugo-winning author" on future books whether you got Best Fan Writer or Best Novel - and you have a higher probability of getting Best Fan Writer. Remember the Hugos are a popularity contest.
I think I've seen the same work nominated in separate categories in past years. Not sure. Ask Keith Lynch.
This year I'm a supporting member of WorldCon for the first time, and I noticed that the Hugo's have a category for Best Fan Writer ("Any person whose writing has appeared in semiprozines or fanzines or in generally available electronic media during 2010."). I do believe Harry Potter and the Methods of Rationality counts, and I plan on nominating it. Even making it onto the ballot will probably expose it to a wider audience. Is anyone else here a WorldCon member and thinking of nominating MoR?