I thought the weakest part of the ship was below the waterline. The ship sinks faster if you hit his ammunition stores or (in the case of a merchant) boiler rooms. In addition, the ship will invariably always sink if you hit it low in the water so he takes on water as she tries to escape.
So I'll say the opposite of what's been said above. AIM CENTRE and AIM LOW. (Unless you're playing with the TMO mod).
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