Yeah it seems like there are usually 2 pieces of contraband in each pirate ship. Which is sort of a pain if you want the ship and you've got to scavenger hunt it before going to a settled system.
Taking ships is not worth the hassle. They don't give you much money when selling and they'll dump their entire pool of items on the ship into your cargo, which is an absolute pain to clean up.
There is a way to register them for less money. Get in the pilot seat first and then after that go to the main menu of the game and pick your ship in the lower left. There will be an option at the bottom to register it for less money. Not sure why.