The history of ninja is incredibly difficult to work out, because it begins with asking the question, "What do we mean by ninja?" and then, "Did ninja exist?"

This thread How many koku would a ninja in medieval Japan get paid for a typical assassination? is a different question than yours but my answers on that thread are about the reality of ninja.

We actually just yesterday had a another ninja thread where I followed up on the first post I linked you.

If you have any questions about those posts/discussions, I'd be happy to answer.