Eeeeeh with all the ninjas being seen as betrayers and exiles, I can see why many ninjas are without 'masters' or employers. I mean, being hated by your own people can make it difficult to come out and say 'hey I'm a ninja and my people may feel my fellow ninjas have betrayed them to the Empire but can you employ me anyway?'. Even for Eorzeans, learning that happened from another Doman's perspective may cause a lot of them to feel mistrusting toward ninjas. Heck, other ninjas may be mistrusting of other ninjas because they don't know who did what.
