There are a few layers to this:
1) Intel, basically when a route is planned they know which areas to avoid which decreases the probability of a pirate encounter.
2) Lets say you are unlucky and do encounter pirates coming for you. Just because a ship is large doesn’t mean it can’t sail fast, so trying to lose pirates by heading full steam out to open seas is a viable option.
3) Large cargo ships especially if they expect pirates have water cannons around the deck. These can spray sea water at high pressure making it near impossible for anyone to board.
4) If all these measures have failed usually ships employ armed guards. I have met a dude who used to be a mercenary and told us he was most doing guard duty on cargo ships.
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