You aren't really using the clay bar on carbon fiber, you're using it on the top clear coat, which should be fine -- that is unless you just have the factory gel coat and skipped the part where you were supposed to get the hood clear coated!

If you just have a gel coat on it, use Meguiar's #49 gel coat oxidation remover and be very careful with it. Comes in a blue bottle, might have to look around a bit for it, check boat places.

Most "carbon fiber" hoods have only a thin layer of the cf stuff on top of a fiberglass hood. Fiberglass is translucent, cf is opaque.