The mother ship has an owner and that owner may not be aware of the ships extra curricular activities. Sink the mother ship you owe the owner a new ship.
Before firing to sink the mother ship they would also need to make sure there are not people on board being held against their will. Attempt to board a suspected mother ship with drugged out pirates and you invite harm to come to your boarding party before they even see the whites of their eyes.
Those skiffs were tracked and it was obvious to everyone nobody was on board so they were sunk without incident. Arbitrarily sinking the mother ship could get real messy.
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