from historical point of view: japanese have expanded along pacific very fast and they lacked of transports between islands. They used anything, even raft boats to carry war equipment from one island to another.
from game mechanical point of view: Sampans are considered hostile merchant, all of them not just a few. When youre spotted by one (it doesnt matter sampan or an 8000 tons merchant) the chance that enemy planes appear among you will be greatly increased. You will get spotted when you attack with the deckgun.
So you have two options.
1. If you are close to objective on secret mission or in shallow waters avoid them, remain hidden if you dont like finding yourself trapped.
2. If you dont care about being spotted, sink them. After all they are enemy tonnage.
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