Not so for the third. More likely an operator came up out of the water and shot the third pirate through the back hatch simutaneously with the shots fired on the topside pirates.
Certainly we will learn more facts. It seems to me that considering negotiations were underway, and I am now reading the navy was towing the lifeboat, that the decision to kill the pirates was pretty gutsy and the US captain deserves credit as a real hardball player who did not lose focus as to who the bad guys were.