No, but neither term was in much use historically. No, you are off the mark. There seems to be no attempt by the ninja to make them seem rather supernatural. That would make them a threat. No, popular culture during the Edo period seems to be a big source for the idea that they were supernatural. You know how media exagerates things for effect. There are some cases like the death of a Shogun while in Koga from disease. He most likely died from bad sanitary conditions, but in an age where magic was thought real- there was some talk it was a spell. Remember, the Iga and Koga regions were known areas surrounded by paranoid folks. If these warlords thought that their neighbors were hiding mystical abilities and might come after them, they would be more likely to launch an attack before that could happen. The ninja tried to not draw attention to themselves or any abilities other than gathering information. In fact- unlike Hollywood, that is about all they were really known for at the time it seams.