The Iga clan was the strongest shinobi clan, but Charlie had nearly wiped them out in the Tokyo Rumble.
The remnants had managed to change their strategy in time, recognizing their position and swearing fealty to the Ito family, sparing them the fate of destruction.
Naturally, Tokyo Rumble was itself a clandestine free-for-all among different clans and mob outfits, so not many were aware of the Iga clan defecting.
In fact, the Iga clan had actually been planning to buy time through defection