I'll correct myself as well, looking into it the residuals issue was a problem apparently for all three movies, not just RotJ, that was just the incident I was familiar with. It's bad, but I just wanted to point out that it was an issue with residuals not his overall pay, and wanted to make clear that it's not that he wasn't paid at all.
I also imagine Fox would be a lot more hesitant to screw over Guinness than Prowse in that regard.
Edit:
Lucas' reasons are his own, he did have known frictions with Prowse, and it may have been a personal decision, but it's also important to remember that the scene wasn't just an unmasking, it was an acting scene as well. Anakin had to show remorse and love for his son in the final moments as well, and Prowse, whose background wasn't in acting, may not have been deemed ideal.
As an aside, Prowse was shown to be Vader unmasked in a different scene, Empire Strikes Back. That's him with prosthetics attached to the back of his head.