Was not my counterfactual scenario. It was someone else describing a counterfactual where ninjas are travelling by sea to a ninja-convention. My only contribution there was to (implicitly) assert that the counterfactualising operation that preserves the most probability mass to produce that scenario would not result in ninjas travelling on unarmed ships.

I edited that; I think the daimyos did have their own navies. I'm not actually certain about that, though, and I don't feel like looking it up. Maybe someone who knows more Japanese history can contribute. In either case, I don't think it's possible to say which is more probable, since whether they book passage on a merchant ship, or are sent with a naval ship by a master who controls both, depends entirely on the circumstance we concoct. Historically, they could have done both, if daimyos did have navies.