being a ninja just means you can sneak. not neccessarily more skilled fighting. sam originally died from fighting nobunaga when he was not transformed yet. i don't think oni3 nobu is stronger than oni2 before transforming.
jubei beat dantess whose more skilled than sam(gameplay wise) after he mangaed to take down the sheild. he trained his granddaughter, jubei akane yagyu whose a pretty ninja like
sam gets badassness points for showing that he still kicks ass way past his prime.