I've played with this Deck for a short while now, and it is definitely missing something, but I know it has so much potential...Plus it's a really fun and original idea. Below I'll discuss my usual strategy and motives with this Deck and of course ask for advice on how to improve it.
A general rule with this Deck was that I wanted to only use "Ninja" cards, or at least as many as I can without using outsiders such as "Freed", because I want my monsters to get the full use out of effects such as "Masked Ninja Ebisu" or "Armor Ninjitsu Art of Freezing".
My favorite amongst them is "Hanzo". He is basically "Reinforcement of the Army" in Monster form, and also has the added utility of searching for Traps - which I have many of; this is to further exploit the effect of "Upstart Golden Ninja". I've found his Monster-spamming abilities to be very handy.
Although summoning the Xyz Ninja or "Dragon Ninja" is highly satisfying, I've noticed that a far more efficient strategy is simply getting "Goe Goe" and "Ebisu" on the Field as soon as possible to exploit their LP-piercing and Spell-phazing effects.
My friends have praised the pseudo-"Cyber Dragon" utility of "Earth Armor Ninja", but I find his highly inferior ATK tiresome. Although there are times when I am blessed by him and "Flame Armor Ninja" within the same hand, usually I can get my Rank 5 Xyz on the Field with the help of two "Flame Armor Ninja". Notably, "Number 12" is the far superior Xyz Monster, protecting my whole troupe from whatever my opponent may have up his or her sleeves.
I find "Sr. Silver Ninja" to be the more desirable high-level Ninja, with his ability to swarm my field full of useful monsters. He can even bring back fallen Xyzs, but not "White Dragon Ninja" (sadly). When I can get him onto the Field, I know I have an advantage provided he lives (And often even if he doesn't)
The major weakness of my Ninja are the inferior ATK of most of the Monsters, and no reliable way of boosting them. "Fuhma Shuriken" is nice, but it's temporary, and only affects one Monster at a time. "The A. Forces" also looks rather insignificant. "Solidarity" would mean I'd have to get rid of my Dragon Ninja (and effectively "Super-Transformation").
Speaking of "White Dragon Ninja", my Deck runs into massive trouble if I happen to draw one (or both) copies of this Monster into my hand, because it effectively makes "Super-Transformation" useless.
Here are cards I've considered adding to my Deck or otherwise fitting into it somewhere...
"Recycle" - To keep a steady supply of "Ninjitsu Art" cards at my disposal. "Hanzo" could grab them from the bottom of the Deck.
"White Ninja" - This guy could also kill Set Monsters, according to his effect. He'd be an alternative to "Sasuke".
"Strike Ninja" - Horribly cool-looking, but I rarely got to exploit his temporary vanishing effect.
"Uria, Lord of Searing Flames" - Instead of using "Alchemy", I thought perhaps the Continuous Traps clogging my Field could be the perfect setting for this Sacred Beast to rear its ugly head.
"Double Summon" - Being able to place "Goe Goe" and "Ebisu" on the field simultaneously (or any two Ninja for an automatic Xyz Summon) would be a nice touch.
"The Tyrant Neptune" - Since Ninja as an Archetype mostly lack pure ATK power, this fiendish Reptile could be my 2-Tribute beatstick in place of White Dragon Ninja. Notably, absorbing Goe Goe's effect would be quite effective.