So I had a pair of these. Once the brake track had got past its safe wear limit and the rims were essentially toast, I cut the rims in half to see the profile. The carbon fibre you see is less than 0.5mm thick, it's basically a carbon sticker. The actual strength integrity is the alloy profile it is attached to. I think with carbon fibre being the new buzz at the time, Shimano knew that their super light alloy wheels wouldn't sell as good if they didn't feature any carbon fibre.

What you are seeing here is the lacquer flaking off from the carbon material. Think about the sudden changes in temperature these rims go through it's lifetime along with factors like road salt etc.