I just played the Rach 2 up to speed with orchestra a month ago. I crack my knuckles, therefore speed is not adversely affected. I have not observed any other adverse effects either. I also crack my back, neck and many other joints.
When you crack your knuckles you are actually releasing pressure on the joints. In all probability you are not doing any damage to your joints, tendons or any other part of the anatomy. Now if what you're doing is actually cracking your tendon on another part of the anatomy, then yeah you will have problems. I don't think this is what's happening to the majority of joint-crackers, though.
I am not a doctor, but this is what I've learned over the years.