Pirates usually didn't kill the entire crew of ships they captured (although they sometimes did) mostly because they wanted to encourage other merchant ships to surrender peacefully instead of fighting to the death to avoid capture, which they would undoubtably do if word got out that pirates would kill them even if they surrendered. This was the purpose of the black flag or skull and crossbones flag that pirates used in the early 18th century. It was a signal to ships that they had a choice to either surrender and be spared or be killed once the ship was taken by force. Some pirate flags even depicted a man holding a cutlass in one hand and an hourglass in the other, making the meaning very clear. This was so terrifying to most merchant sailors, that they usually surrendered without a fight, and in return they were usually not killed. In fact even when they did fight back and were eventually captured, the entire crew was usually not killed. I made another post here that discusses this and some of the ways that sailors could be treated after they were captured by pirates.

EDIT: Some pirates did successfully impersonate legitimate merchants and privateers. Probably the most successful one who did this was Howell Davis. He used this ruse to successfully infiltrate the British fort of Gambia in Africa, get himself invited by the governor to dine with him, and then take the governor and his associates hostage and successfully extort a large ransom. However, eventually when Davis tried his ruse on another island the authorities were alerted to his real identity by an escaped prisoner and he was ambushed and killed. Pretty exciting stuff. I made another post about this.