It's really quite easy. If you can read kanbun, just pick up the extant primary scrolls and books about ninjutsu. Pretty easy to do a Japanese search for the source materials and where they are kept(National Diet Library, etc). Kacem Zoughari's book also has an extensive bibliography. However, secrets were kept secret by not writing about them or writing in a way that only people with certain other knowledge could read them. Beyond that, there are a few academics in Japan who are researching ninjutsu in this way. Correspond with them and you might be able to get some insights.