Two reasons:
1) Imagine throwing an apple at someone who is sitting just under the surface in a swimming pool. The moment your apple hits the water, it’s going to immediately slow down. If it hits them at all, they’ll barely feel it because the moving apple loses so much of its energy to the water. In exactly the same way, even if you could get a good shot that doesn’t just skim on the water, it will lose most of its energy before it hits your target.
2) Generally, no one wanted to sink the ships they were fighting. If you disabled a ship, then you could take it with you as a prize – ships were worth a great deal of money and governments would pay prize money for captured enemy ships. Shooting at the rigging or rudder left a ship unable to manouvre, but readily repairable once it was captured, but a shot under the waterline could sink it.
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