You don't need ninjas. You need an army.
In honesty a particularly scary force would be:
Katsumoto Takashi (12)
2x Guardsmen of Ryu (8)
2x Spearmen of Ryu (10)
8 Models with plenty of ways to get pass tokens so you can control the flow of battle, you also have two ways of performing Commands or Orders which can be brutal if done right. Here is an example 1st turn Hanso and Junichi Focus. Katsumoto Orders them, so they can move up a bit. You then have on turn 2 enough Ki for Move It!, Battle Stations and Tactical Master allowing you to move your force up for free and attack simulatously. Refresh and then do it again.
Also I can't find anything (granted I'm at work at the moment) but nothing says you can't stack multiple Commands as the Command ability itself is a simple action
To say nothing of the large Leadership area of Katsumoto, the wide range of Brave in the force (and a way to remove frighten tokens anyway) and while there isn't a really big hitter you have 2 guys with guns that can get close for free and then still shoot