My horse does the same sometimes. I believe it's just down to balance, since she often shifts her weight and doesn't like to stand still. It's unbalancing for her to only stand on three legs, so she sometimes slams down her hoof to support her weight when I'm trying to clean it.
Some retraining may be good using positive reinforcement.
Feel around his legs to look for a reaction, whether that's a slight head raise, a glare or even a flinch. This could be a sign of discomfort or pain. If he reacts when you feel around his legs and hoof, I would personally call out a vet. Otherwise I'd leave him be. Also check for lameness.