Heh, that's not what the shinobi were or their primary role. The military stuff were their day jobs, so to speak. The art and what it does is much weirder than that. The Iga lineages were said to specialize in the small team tactics, whereas the Koga lineages were much more interesting.
There are pretty good historical evidence showing legit bushi (legit, as in being backed by the ruling power) who went undercover on covert ops. They may or may not have had anything to do with the Iga or Koga folks at that time. One of them ended up carrying (or founding) a famous sword school.
To be fair, there are spec ops folk who train with lineages in the US. Does that make them ninjas? I suppose so.