To be quite honest, I have trained with senior-level people (5- or 6-dan) in a certain well-known major organization who have done the exact same thing you described here, so it would make sense that the lower-level people are copying them and doing the same thing. If your shihan only teach the nage side of the practice, and your senior people don't understand the uke side, then it's unlikely that you are going to have your junior people spontaneously learning these aspects of ukemi.
I completely agree with you. This is a failure on the part of the Shihan or other senior instructor(s). It's one thing to leave someone on his own to figure things out. Its quite another to keep promoting him and letting him open a dojo when all he is doing is passing on very bad habits to his students and ruining another generation of practitioners. I think it is wrong. I have publicly objected to this repeatedly. The transmission is largely broken.
It is our responsibility to fix this. No one else's. The folks who created the problem will not be the ones to create the solution. Much of the discussion on the forums here revolves around different folks take on what the issues are and what the solutions are. That is why there is hope. The folks who created the problems with the transmission are not discussing anything. They are not looking for new ideas or alternative methods. They decided these things long ago and are not interested in change. The best of them will at least give you some encouragement if you show signs of trying to do better yourself. The worst of them will actively stand in your way.
But no one except us will fix it. And it will take a community of people who decide to find a better way, not just isolated individuals. It will take people deciding that they need to look beyond the confines of the world as revealed by their teachers, to risk being criticized by the establishment. I am not saying break with the establishment because that is the surest way to end in obscurity and change nothing. But I am saying that it is possible to work within our various systems and organizations to slowly change people's ideas about what they are doing.
The entire old guard of American Aikido will be gone in the not too distant future. The Japanese and the American teachers who have pioneered the growth of the art here are all close in age. Who will take over when they are passed on? It is us. And we need to think about what we would like the art to be and how we expect to take it there when that time comes.