Short exercise. Does anyone actually think pirates stand a chance against professionally trained assassins? I thought the only reason people defend pirates is because it's a way to say both of them (or their identity-memes) are just so damn cool.

What are we talking about here? Ninjas didn't normally kill in open combat (nor did pirates if they could help it) and pirates didn't generally fight in set piece battles on land. In order to give a serious answer to such a question, you would first need to specify a combat situation: 17th century-style naval combat (of which the outcome would be largely dependent on the state of Japanese versus Portuguese maritime technology), open field daylight desert island team combat, single combat (with or without firearms and at what distance?), coastline castle siege, covert assassination of captain/quartermaster aboard a ship, etc...