Thumb pain is quite common among video game players. Back in the 1980s it was associated with Nintendo and called nintendonitis. Besides pain, the thumb can be unstable because of lax ligaments. Thumb pinch strength is greatly reduced.
There are many types of keyboards designed to reduce the risk of muscular pain. Some are split in half to make it easier to reach the keys. Others have rearranged the keys or put a soft bar between you and the keyboard to support the wrists.
You can even buy software that reminds your son to take regular breaks. The program gives on-screen examples of the exercises that can be done to stretch and protect against repetitive motion injuries.
However, just changing a keyboard is not going to solve the whole problem. The thumb wasn't really made for so many hours of pounding and overuse. Limiting computer time is also suggested though not very popular among video gamers.