About a month ago, I was sitting in the home of the Momochi family in Japan. (Momochi Sandayuu, one of the few acknowledged ninja leaders was born there). The current head of the family was my host, and I had a wonderful chat with him... including finding out that Momochi Sandayuu was a Samurai of the Daimyo Class!
So, if you were a daimyo, in charge of other warriors, yet with clandestine ties, and your local ruler asked you to help eliminate a 'problem' you had choices:
1) mobilize 100 samurai, with armor, with food, with gear, etc
2) ask your already-in-place "agent" to poison the well water...
which is more cost effective?
He also likened it to the modern military. He noted that there is NO modern military in the world that does not have a clandestine side of their operations. Hatsumi Sensei has noted that perhaps only one war is on the records that was waged without use of "alternative" agents. (He also tells at least one story of an assassination by a ninja - to keep this answer relevant to the thread).
Thanks to Mr. Momochi for a great time. You can see him in the soon-to-be-released documentary:
Shinobi - Winds of the 34 Generations.