As for the question of what ninja actually did wear, ask yourself this : what does the average spy wear ? The answer, of course, is whatever it takes to blend in and get the job done, whether that means shorts and a T-shirt, military fatigues, or a suit and tie. The same was true of the ninja. Hiding in plain sight was their entire modus operandi. Most dressed like farmers, both because it worked well as camouflage in a nation of farmers, and because most of them really were farmers. A real ninja would laugh at the portrayal of an intruder tiptoeing across a rooftop wearing black pajamas in broad daylight.