A few years ago on Corner-Carvers, there were some posts showing Corvette factory wheels cracking across the spokes and some where the spokes and hub separated. In those cases, the wheels were powder coated by the owner and not the factory. The wheels may have been the optional C5 magnesium wheels, but I can't confirm. The general consensus was to not send wheels out for powder coating. Factory finish is ok, paint is ok (white being the best for crack detection), polished is the best (until you scratch the surface and get a stress riser), and chrome and powder coating being less desirable. This was for wheels seeing high amounts of stress and heat. Seeing this type of failure on the street is not something I have seen much of, but believable due to the powder coating.
There is no doubt that heat and time change the molecular structure of the material. Cleaning agents along with heat can easily change the surface condition of the material and surface tension is important to reducing stress risers. A great example is glass, scratch it and it will break there because you gave the crack a starting place. I would bet most powder coaters that handle small batches are not going to change their cleaning or baking process for aluminum. Aluminum wheels would be ran with whatever steel parts being ran that day. This could easily cause too high of heat and improper cooling, which will greatly affect fatigue strength.
It is very common for professional race teams to x-ray and use dye penetrate on their wheels after races to look for cracks. Most teams probably have a known number of cycles before they scrap a wheel.