J.L.
More than likely it's from the thumb sucking. I sucked my thumbs until I was 5 or 6, by the time I quit I had these huge wart looking things on my thumbs. No evidence of them now though! I eventually got self conscious about it and decided to grow up.
No amount of hot sauce or anything nasty would do the trick, it's like trying to help an alcoholic. You're not doing any good unless he wants to be helped. I remember pretending to enjoy all that nasty stuff... while desperately sucking trying to get rid of it all! Hopefully your son isn't as headstrong as I was. Good luck!