Appearing as yourself in a documentary or any film, for that matter, is fine. Archived/Stock footage is not. This means that if the footage of a person was not originally shot for the film in question, then it does not count as an acting appearance. IMDb makes the distinction by listing archived footage appearances as just that "Archived Footage."

Since Bush did not appear as himself in original footage shot for Fahrenheit 9/11, he doesn't count as an actor in the film. But say that we actually had original footage of him captured by Moore and crew, then it would count.

Maybe I'm wrong, but I don't recall him actually appearing in original footage. All I can remember is archived footage of him. Correct me if I'm wrong.