J.,
I don't have any "magic" for you -- just some possible reasurrance. My son, who is now almost 21, sucked his thumb for many years. Yes, it looked horrid, callused, nail damaged, etc. And, like your son, he only did it when tired for comfort. Finally, after trying everything that came my way, I just let nature take its course. He did, indeed, stop sucking his thumb. Yes, he did have braces; but, so did both of my younger children neither of whom were thumb-suckers. I would encourage you to watch his thumb just to make sure it stays free from infections (the human mouth is a dirty place).
Good luck!