This doesn’t seem to be too huge a problem, for which there could be a simple or complex solution.
The complex solution is the development of a new cluster munition like the CBU-97 Sensor Fuzed Weapon, which dropped 10 munitions, each of which had their own parachute and guidance system, looking for the tops of tanks on the battlefield and steering to it. It then used a shaped charge to blow a hole through the lid on the turret.
Its munitions were far larger and armor piercing, than what you would need to blow a hole a few feet across through the hull of a small boat. So you could put a lot more such munitions in a single cluster bomb.
A much easier technique is to use an airburst propane bomb.
At altitude over the target, it spins and sprays a big cloud of propane, then ignites it. This causes an implosion that changes the air pressure in about a half square mile area from 1 atmosphere, to near vacuum, to a dozen atmospheres in a second or two. This is harmful to people, and would likely knock out every boat in that half square mile area all at once.
Seeing dozens of those things being fired from then detonating 2000 yards away from a ship would be impressive.