You do know that the new world champion in duel links used ninja right? He didn't use any red eyes, Phoenix or gravekeepers. Be did use Toons in the first of the final matches, but so did he's opponent, and in the second round Toons lost to ninja.
curse of anubis, windstorm and sphere kuribo switch toon monsters to defense mode and sasuke gets rid of them.
Your Econ and sphere kuribo argument is dumb. If toons don't get toon kingdom/table of contents/planet pathfinder they lose. If Red-eyes bricks, which is pretty common, they lose. If naturia doesn't get one it's two level monsters they run, they lose. See where I'm going with this ?
I used ninja pretty often and when I face toons I often use turnabout and set the toon monster face down and pop it with white ninja afterwards. And red-eyes pretty much give a lot of deck hard time so its not exclusive to ninja but again I use turnabout with red ninja for phoenix well I never really have problem with them to be honest.. Gravekeeper rarely bump into one so I can't really tell
I've never lost a single match against ninja decks using Phoenix decks. Ninja decks heavily relies on spells/traps like control decks which I've never lost to also. Turnabout is a dead card if you don't summon armed ninjas so it's garbage.