Well, piracy was a huge thing in Japan and China and so on, so if there were any conflicts between them, they could have been recorded. But I don't see why they would have been- typically, there was no significant benefit to killing a pirate captain (rather than sinking his boat or hanging him and all of his crew), and so assassins would only be employed against people whose deaths were meaningful enough (generals, title-holders, etc.). Similarly, I doubt ninja would transport valuable cargo all that frequency, and typically it was Japanese pirates preying on Chinese vessels anyway.

I mean, pirate just means "sea bandit" but evokes the image of mostly European sea bandits at a time when navies were based far away, coastal land was essentially free, and cargoes were really valuable, because that's when there was a veneer of excitement over lowlifes murdering for fun and profit.