I've read that one of the biggest causes of failure is where the powdercoater heats the rims up to well over 700-800 degrees to bake the existing coat/paint off. Also incorrect sandblasting can cause minute valleys/peaks in the metal that weakens the structure. I think the actual powdercoating process itself is unlikely to cause catastrophic failure, providing the preparation is done correctly.

That being said, one of my mates at work is studying metallurgy, and he said the powdercoating process will begin to alter the metallurgy of the rim, but its so minor that it will take a very long time (20 years maybe) to see any effects, if at all.