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From what I can tell the flagships that sink before you get to board them is because you (accidentally) killed the NPC crew with your cannons before you got a chance to board the ship.
Once the ship goes into "ready to be boarded" mode you can't damage the hull further. The ship is just waiting to sink based on the NPC crew being defeated and if someone happens to pick off the crew with the cannons prior to you boarding the ship will sink.
Similiarly if you have boarded a ship and are fighting the crew...a passerby can help you pick off the crew with their cannons and allow you to capture the flagship quicker.
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