What if it wasn't really that secret at all, but was simply esoteric knowledge that made a somewhat clunky, innappropriate fit to martial applications due to steep learning curve and not much usefulness versus the time and resources required for training? Until the Meiji period when there was no longer a caste of professional warriors who needed real combat skills to keep society functioning?
Good question, and one that others have asked, myself included. My conclusion is that it depends on how it was taught and transmitted, and that depends on the teacher. If, say Sokaku Takeda learned it in a very esoteric way from Saigo, but was, as is believed, a genius who was able to extrapolate the essence and apply it to his technical martial skills AND be able to physically transmit it to his (selected) students in that way, then the learning curve is not that steep or long. Sagawa is quoted as stating that he "understood aiki-age" (meaning, he understood the Chinese concept of Peng) when he was 17, from training with both his father (also Takeda's student) and with Takeda himself. The Japanese teaching way is the classical Asian one that is more physical teacher-to-student transmission than verbal instruction.
The available information -- interviews with students/former students, eye-witness accounts, etc. -- indicate that such information is, in fact, quite proprietary and often secretive. That's the way of that culture. The "secret secrets" were taught only to select individuals. Or, through no intention of withholding and more due to the individual students' particular capabilities, focus and needs, the skills were taught to varying degrees so that no two students had exactly the same set of skills, some had more of one thing than another, some were lacking certain aspects, a very small number had the "whole package." Some just plain didn't get it, and went elsewhere (allegedly, Tohei and Shioda, for example). This is evident in Morihei Ueshiba's own pre-war Daito-ryu students.