Most of these mother ships are captured merchant or fishing vessels. Now if the crew cannot escape on the lifeboats or lock them selves in the citadel (sort of a panic room with a radio, normally the ship's engine room) its highly likely that they will be captured and held by the pirates. Any attempt at seizing the mother ship puts them in grave danger and should only be attempted with the best possible planning in place.
IMHO detection, avoidance and deterrence of pirate action groups is the best bet right now. Starting a war with them would be very nasty.
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