I had a thoroughbred that had high withers. The only issues we ever had with her were finding and making a saddle fit on her. Other than that, there are no other issues I've ever heard of or dealt with.
you are all right on about the saddle issue...tried many used saddles on him at the ranch and none fit, ended up bidding on a big horn endurance (similar to the tucker endurance he wore before), still waiting for for it to arrive to see if it a good fit!
I am glad the hear that there are no other issues that are obvious.