But certain ninjas are semi critical to certain mains, which means if they are banned, then the optimal setup would require a main change. Forcing someone to do a main change is... just horrible.
Just think, how many people would use water main if sailor sakura is banned? Or, god forbid, sailor sakura AND mei. There are VERY few water main who uses neither of those.
Also, some ninjas are rather exclusive and an advantage people paid money for. Banning those isn't exactly fair.