According to the obligatory Simpsons wiki, he appeared in one of the comics (which is considered "non-canon," as if Simpsons has a strict canon or something) and also he was going to be the villain of the movie but they decided to go with a different character who had the same voice and mannerisms.
I don't care if he reappears or not because so far as I care, the original Hank Scorpio episode was the last Simpsons episode truly worth watching and would have been a perfect series finale.
I sort of figured that the head of the EPA in the movie was Hank Scorpio in some form, probably just because of Albert Brooks. In case you haven't seen the movie, there's certain parallels, but Mr. Scorpio wouldn't do that! Not to his friend Homer! I'm sure some of you guys have too, but I had a boss who was exactly like Hank Scorpio. Nicest guy in the world doing something pretty soulless and inherently evil, but he didn't blow up the Eiffel Tower, as far as I know, but would've in the wink of an eye.