It is very likely that several hundred years ago, these skills were quite prevalent, and varied considerably from ryu to ryu (with, I will agree and emphasize, the same core). One bit of evidence for this is that there are a number of stories of sword masters - with no major record of jujutsu training - who get in a beef with sumo wrestlers and dominate them. There are vague references in these stories to body skills, etc. An example would be an account in Lives of Master Swordsmen, regarding the founder of Hokushin Itto-ryu. I can think of almost no koryu practitioners today who would have any ability to stand against a medium level amateur sumo player.
It is very fair to say that these skills were almost completely lost by the end of the 19th century - otherwise, Takeda Sokaku would not have been regarded as unique and remarkable. (BTW - I believe I have traced where Takeda got these skills - I'll be releasing this info soon on Aikido Journal and then later in a book, Hidden in Plain Sight
Evidence that the frame without the heart is still there is Akuzawa - in what he's "recovered" from Yagyu Shingan-ryu. I'd seen the top folks in most of the lines many times, and it was obvious that they just had motions, not the essence. I do not know if Akuzawa has actually recoved pure Yagyu Shingan-ryu essential training, or if he used the kata (shape) of their basic movements and "filled" them with discoveries of his own, an amalgam of all he's trained.
There are also a few schools which have extant bodyskills training - Kuroda Tetsuzan, for one. I can think of several others - and honestly, I would be breaking a promise to even mention the names of the ryu - without trust, the people in question would not have even told me anything about it. But I can think of a few schools that actively and dedicatedly train in solo breath work.
But most have totally lost it. Several generations ago. And it is unlikely that it could be recovered - at least as it was.
The whole secrecy issue - the dilemma is that if someone is taught something under a promise of secrecy, then one is a betrayer to reveal it - unless one has the authority to do what one wants with the tradition, being a lineal successor. A dilemma, nonetheless - because, there can also be a faux-secrecy, "clubbish" clique in many koryu, when they have little to nothing worth hiding. Having no fear of being tested, one rests on one's assumed laurels. Hence "koryu-snob" - which I've seen both in Japan - (a lot) and on the internet, as well as "koryu-wankers" (my term - I DO have a legacy!)
BTW - "Aiki as ura of kiai." This formulation is Mochizuki's - and further, kind of common in aikido circles. But it is not general, and is kind of a "throw-away" line, to attempt to distinguish "aiki" from kiai, a concern of aikido folks more than any others, and comes from a limited understanding of kiaijutsu.
Much more common in koryu is a more sophisticated and detailed delineation of kiai, using gogyo (five element theory), for example, with variations of yin/yang, etc., association of kiai with seasons, body parts, etc. See Jikishin Kage-ryu, for an example. Again, a lot of this info has been lost, but it is intimately related to the development of body skills - what is emphasized in kiai, as opposed to kokyu or ki cultivation is a simultaneous organization of one's own body and psychological effect on the opponent at a distance - as should be the emphasis is in weaponry.
Bottom line - most koryu are truly Kage-ryu - mere "shadows" of their former selves. Further, those few ryu that do still have that knowlege are usually quite protective of it - which is probably the reason it survived in the unique permutations of the basic skills that they developed. Further, a lot of ryu are running on fumes - claiming special status or skill based on what people used to know and be able to do - not what they can do.
My final evidence - it was my firm conviction that the two ryu which I am licensed to teach had no history of "bodyskills," in the manner that is being discussed on this forum. But as I am learning a little about these skills elsewhere, I am starting to see, inherent in some things I took for granted, that these skills might have "used to" have been there. It must have been a long time ago, however, as Sagawa Yukiyoshi, a menkyo in Araki-ryu, dismissed it because it didn't have, in his view, "aiki."