I'd go see a doctor if I were you =.=
Muscle pain is ok in most cases as they regrow regularly. Joint pain is a lot more complex and it can take a lot longer to recover from, or if you're unlucky, serious damage if left unattended.
Carpel tunnel is caused by compression of nerves (usually around wrist area) so the effect should be more global. Patients usually notice numbness, rarely a local pain.
You're probably slowly dislocating your thumb by hitting the kb repeatedly with a lot of force. But then again, I'm not a doctor and people need to learn that internet is not a place to get answers when it comes to medical problems. I'd go see a doctor.