I have dived many of the world's coral reefs. Several points.
1) Man has been damaging reefs on an epic scale for centuries. In the Middle East the reefs were mined to produce building blocks that cities were built from. Thousands of ships have wrecked themselves on reefs. Lots of war has happened on reefs. Dynamite fishing of Philippine reefs has done immense amounts of damage. As bad as rainforest depletion.
2) Reefs are living things and thus are amazingly resilient. In fact they can be manufactured. Put some concrete shapes on a sandy bottom in the tropics and pretty soon it is colonised by coral.
3) These practice bombs in the enormity of the Great Barrier Reef are far less than insignificant. Like a grain of sand on a big beach.
4) Recovering the bombs would be relatively simple.
5) The bombs could become a tourist attraction.