"Clothing used was similar to that of the samurai, but loose garments (such as leggings) were tucked into trousers or secured with belts."
The purpose of those flags is to signal who and where you are. Neither of those goals aligns very well with what ninja do.
http://en.wikipedia.org/wiki/Sashimono
"Clothing used was similar to that of the samurai, but loose garments (such as leggings) were tucked into trousers or secured with belts."