The thing is, they pull videos based on copyright claims from ANYONE. I've seen One Piece videos pulled due to copyright claims by 4Kids, after FUNimation got the license. Probably because somebody just reported the video and cited 4Kids, and YouTube just figured "Okay, we'd better take this down before we get sued" without researching to see whether or not 4Kids even had a right to claim copyright violation. So while its understandable that YouTube doesn't research every claim, that doesn't mean that these videos were pulled do to an actual claim from Toei.
This.
A while back there was a douchebag Sonic Fanboy named Spax3, he took down criticism videos for "Copyright Infringement" of his little company that has no copyright standing.
Anyone can take down a video and claim it as copyright infringement, even if it's just a guy in front of a camera talking with no images, music, or other video.