Being able to see her isn't really what convinces me that Fluttershy is not a real ninja. It's the fact that she's simply just too gentle to be a ninja. My theory is that perhaps she tried and failed to be a ninja.

Although, if Fluttershy were a real ninja, she would be the most adorable ninja in existence. And she would also be the best ninja in existence because all other ninjas just wouldn't have the heart to kill her. If she were a Naruto style ninja, she'd probably end up being a medical ninja.