Were ninja similar to other secretive, cult-like orders of the day, perhaps like the hashishin, or assassins of the Crusades?
I don’t think so, because the assassins had a strong, powerful jihadist sense, very deeply rooted in the religion, whereas the ninja were not religiously driven. The overlap came in that the ninja wanted what was called “right-mindedness.” They had to have the correct attitude in order to undertake what they did in defense of their villages, their masters and themselves. What they did was train in a local belief system, which was Shinto and called shugendo, which is really mountain asceticism, which demanded that you undertake training in the mountains and along the streams to hone your body and mind until you are absolutely fit enough to carry out ninja activities.
Did this involve sword craft and flying daggers?
There was never any sort of formal martial training. It would have been from childhood, within the family, learning self-defense. The only formal training I’ve heard of was with the shugendo ascetics who were not ninja. And not all ninja underwent shugendo training.
So is this more of a spiritual process than a martial one?
It was both. Certainly it was spiritual. It was martial in so far as it trained you. There were no martial arts involved, but clearly if you can survive sitting under waterfalls or walking many miles in forests in extreme adversity, it helps you in your training to be a fighting spy.