Although he might be a sort of throwback to Shadow. He certainly does have the work for gil/canine companion/throwing weapons/"I don't give a f*** about you and I'll slit your throat for the asking" thing going on.

Ninjas actually used things MUCH fancier than samurai swords. Most of it would be called "slight of hand" trickery today, but Yojimbo doesn't do any of that. He just throws knives, sicks his dog on you, cuts you with his sword, or chops you in half. Shadow could use elemental attacks, turn invisible, and other things from his throw command. Shadow was clearly the fancier of the two, even if he was not technically a ninja according to FFVI.