Our teacher Ichimura sensei had kototama classes with us, during my first years of aikido - both theory classroom style and exercises on the tatami. I still do it, now and then.
I also wrote a chapter about it in my "Aikido: The Peaceful Martial Art":
http://www.amazon.com/dp/1419658794/
It's not at all a necessary part of aikido, but some simple kototama exercises can add perspectives. The aikido techniques can be done in a kototama manner, with the "chanting" and all. In my humble opinion, it doesn't have to be very complicated or include religious apparatus, but it does include a cosmology of sorts.
Well, it can be described as a cosmology expressed through sounds.
Nakazono sensei wrote several books about kototama. I don't think that they can be found on Amazon, but here:
http://www.kototamabooks.com/