To be clear, coral reefs are essentially collectors/attractors/homes for a huge number of fish species. If you go away from a coral reef (even 50 meters), there is large drop-off in the amount of fish in the water column -- almost none. They are absolutely bomb fishing within coral reefs because there are lots of fish.
Yeah, but the reefs aren't the goal. They're probably mostly not blowing up reef, but occasionally do it it - hence why so many bombs clears so little reef. If it was massively reducing reef coverage, you'd expect to see the method die off once too much reef is gone.
Fishers, I would guess, are aware of fish wanting to be near reefs.