I always thought that the "we're freaks who need to hide from the world" thing kinda loses it's meaning once they realize they live in a world full of aliens, superheroes, robots, Ninja-crime-bosses, demons, and other anthropomorphic animal people. Not to mention they live in a big city full of amazing sights where people are unlikely to notice or really care about seeing Turtle-people running around in it.
But, I also agree that as a group of ninja (with a lot of enemies), they should keep a low profile anyway.
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