Will knuckle conditioning effect guitar

affect*

I would imagine that the repeated micro trauma known as conditioning could lead to abnormal ossification, bone calcification and scar tissue on the tendon. These could effect your ability to play guitar. I wouldn't recommend it but your mileage may vary.

Generally I would call bone conditioning a very bad deal. You are guaranteeing short term injury for the potential of not having an injury in the long term. Though the bone conditioning itself comes with its own long term chance of injury. All martial arts is like this, you are far more likely to be injured training than from the potential crime you could use it to defend against.

Disclaimer: I am not a medical doctor. All advice is educated opinion.

Look up the great artist Django Reinhardt. He was a terrific guitarplayer, but one night, his trailer took fire while he was asleep. His two fingers was burnt off and the doctor said that he would never play guitar again.
But django stuck with his guitar, and he played music and lived on it until he died.
here' a link so that you can learn the story about one of the worlds best guitarists:
http://en.wikipedia.org/wiki/Django_Reinhardt