I think it's one of those things that adults believe will be a problem (i.e. everyone telling me that my daughter will get called Poison Ivy, when no person under the age of 40 has ever mentioned it), that just isn't in the real world. I could be wrong, I just don't see it as being a likely issue.
ETA: And the people that will likely be their bosses someday (people our age and slightly younger, scary!) will just think of Fox Mulder :P
Peter or Richard get made fun of for their name (that goes for the people with the surname of Johnson as well). Also, X-Files started when I was 7 and ended when I was 16. I know who Fox Mulder is but only associate the name Mulder with him. I don't know anyone my age that ever watched the show so I'm not too sure Fox Mulder will be an association for many people.
Thanks everyone. We are real learning to it