I have knee problems - I don't think from just riding. I think more of playing basketball, running and when I used to compete in barrel racing on a short horse I would sometimes hit my knees on the edge of the barrel. (A couple of times REALLY badly!) I was also kicked in the knee by my horse. It does affect my riding, though. I often have to ride without stirrups, or at least take my feet out and stretch a lot. When they are really bad I have a hard time posting and using my left leg for cueing. Which makes it difficult to have a straight horse! However, the more often I ride, the less problems I seem to have.
Don't squat with yer spurs on!