I think the group with practice winning naval engagements would more likely win the naval engagement.

And by this you mean the Navy vessel that is transporting the ninjas would more likely win the naval engagement? (The engagement that the pirates would never initiate because they are experienced in not picking fights that they will lose).

Or are we still talking about the landlubber ninjas who have never learned to sail that are for some reason trying to sail themselves across a sea for conference purposes? I'm imagining them up in the rigging comically trying to sail and needing to use all their ninja agility to dodge the yardarms that are swinging around wildly as they try to figure out which way they are supposed to pull the ropes...

Basically, pirates can beat ninjas if they load up their cannons with idiot balls for ammunition and the ninjas eagerly run out to catch them.