No, the governer doesnt make it clear... When I tried to do that quest on Keth, I didn't know about the ships. Didn't realize they were there until a few characters later. While trying to do it though, I tried to discover what NPCs counted, so I would slay a few of a type (some of them against alignment most likely, though I didnt have DA)... the swaggering sailors? nope. the other sailors walking around? nope. kept doing that with all of the multiple-spawned NPCs. nothing. Governer HAD mentioned something about "merchants" so i even killed a few shopkeepers (definitely against alignment), and nothing. Seemed none of the town NPCs were the right ones. Then on Jaervis, I found out about the ships (and felt like an idiot for not knowing) and killed a few of the crew, checked the quest, and yay! they counted. I think someone mentioned to me that all the crew are dark (the slaves in the hold on one of the ships are lightie).
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Aren't those just sailors? Not all sailors are pirates!
Pretty typically, all the sailors on a pirate ship, are considered pirates. Guilt by association at the very least. I mean, they had slaves in the hold. Governer wants your help to stop them from their business in human trafficking. Whether they are the masterminds running the business, or the thugs working for said mastermind... they made their choice, right?