Say I had a Cranindos with Mold Breaker up against a Graveler. Graveler was holding a Air Balloon. It also had it's natrual Ability Rock Head. I know that Mold Breaker will cancel out Rock Head, but will it cancel out the Air Balloon's Effect too?
No. Mold breaker only affects the ability the pokemon has (graveler's rock head) but since air balloon is an item, it won't work. It's like protect- Mold breaker won't hit.