That's what puzzled TCG/OCG players back when Secret Six Sams are revealed. They're clearly more ninjas than samurais, and even worse part, according to the lore, Ninjas are supposed to be Six Sams' archenemy lol
Then again, I guess they are secretly Six Sams pretending to be Ninjas to infiltrate the Ninja organization? Would have made so much more sense if they reveal that to be the lore.
I do have a theory, maybe they are called samurai because in this world samurais and ninjas are enemies, so even if the samurais had a ninja-like faction that is all stealth and stuff, they would not call them ninja