Old strategy

Faultless
Strategy is when you command the armies. And when you're running around with a sword, then it is not a strategy.
pow

Guys who know the name of the strategy where there is a ninja
Spoilerless a movie of the same name)

Don't know about invisible, but ninjas and other units of ancient Japan there in the strategy Battle Realms.

Maybe it's Command & Conquer 3: Tiberium Wars,there is playing for GBR is the killer (they're a bit like ninjas) who can become invisible,they can fly.

it's not, maybe you know other options?

Something that is clearly associated with Japan, and strategy.