If you stick to shore in waters classified to other biomes, you will not encounter this enemy.
Each ship has different durability levels which determines how much time you have.
In the case of a raft, it only takes two blows for it to go under.
How to get the Serpent scales?
One of the raw materials dropped by the Serpent are scales.
Unfortunately, they sink on the high seas, so collecting them in normal combat is virtually impossible.
However, there is a way to get them.
It is time consuming and difficult to accomplish alone.
This method requires you to have a harpoon.
If the sea serpent is not in escape mode, you could tow it freely.
At night, sail along the border between the Ocean and the land biome.
This way you will be close to shore and able to get there quickly.
When the boat reaches the shore, jump off and head inland.
This will pull the snake ashore.
In the meantime, you might easily eliminate him and claim the loot.
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