I would think that the different woods and their respective stiffness would change the flex of the shaft greatly and have a definite impact. Negative or positive would be in the hands of the cue maker.
The shaft is stressed more than the butt. I think most cuemakers would rather just leave it alone for fear that something should go wrong under use and have their workmanship come into question. I know, that's how I view it. I may change, but right now, there's enough other stuff to worry about.