But since they are wandering samurai, then why not be able to give them land?
Or if some of your own courtiers are unhappy, they buzz off, and may join a ninja clan. Is there any kind of hierarchy in the clan itself? Nothing fancy (rule for life, succession based on highest stat), but depending on the leader, there could be clan-wide bonuses (due to his stats) or clan wide limitations/bonuses: Perhaps you're best friend brother is leader of a clan, he will honorably decline actions against you (or it might cost more to accept). Or if he's your enemy, he'll gladly do you in for nothing.