There are some areas that are fish deserts. Subic Bay is one, but the wrecks are good there. Either they were fished out by dynamite or cyanide fishing, or the local fishermen catch everything before it can swim away. It's their daily food and livelihood, can't blame them, but the resource is fished out. Nearby Anilao is better. Moalboal on Cebu is great still for the sardine runs and the occasional thresher sharks that eat them. Puerto Galera and Alona Beach are not to be missed.
In some areas lately I have seen reef bleaching, dead. Don't know the cause, but coral are the base of the food chain in the sea, and bleaching means fewer fish. Apo Island for instance has fewer fish than in the past and I am seeing a lot of bleaching there. Still a lot of fish, but fewer than before. The island is a sanctuary, only locals can fish using spear or cages, so I don't think that's the reason. Bleaching is a concern.