For this answer I'm going to clarify two terms for the purpose of this answer.
Ninja is a subtype like "warrior". The techniques they employ may not have anything to do with a clan or any higher purpose.
Shinobi is a term almost exclusively used for the Shosuro Infiltrator in the L5R universe. They serve exactly one person: their own personal lord as part of the clan even if not directly acknowledged.
Shosuro Infiltrators are everywhere. They are sometimes deep undercover agents in disguise as opposed to a shadowy figure skulking in black pajamas (but they'll do that too). They can be information gatherers, assassins, or simply well-placed resources if their lord wants to be up to something. But that's the main catch: They serve only their personal lord. Whatever clandestine tasks they are given, they must carry them out and trust that their lord has a greater plan in mind. They don't have to follow any tenet of bushido to get the job done except for this caveat of Loyalty. Most Scorpion samurai are aware that there are agents in the field and whether or not the shinobi in question is in alignment or against their plans will determine the reaction of even their clansmen.
A ninja they have the right to kill outright (although may easily be disinclined to do so) as being part of a lower social caste or try to use as a double agent since there is a strong chance they are simply a mercenary to begin with.