**Tax the hero identity and the secret civilian identity separately.**

If Superman and Clark Kent claim to be two separate people, then they both need to pay their taxes. Any income needs to be reported by both people and they both need need to pay the tax. So any income of Superman/Kent is taxed twice.

This, of course, also hits those villains who also have secret identities while it spares those heroes who operate under their real name. But these are rather exceptions than the norm.