Ninjas are typically silent assassins, not badass anime protagonists. (I'm looking at you, Naruto!) Their deeds are not generally honorable in nature. Historically, they're seen as more of an unfortunate necessity to preserve dynasties. The honorable warriors are the samurai. Although history has shown that the whole "way of the samurai" thing was actually made up for Japanese theater and they weren't historically honorable either.

Regardless, when it comes to modern-day Japan, they love the concept of an honorable protagonist who wins by sheer willpower, even if the odds are stacked against them. Giving their opponent the advantage and then still winning in the end is seen as a clean and respectful victory.