Hello,
We were not given a specific reason as to why some ninjas were excluded from this and some were not. Unfortunately, as always, we cannot provide information on future releases past what is given out each week. I am sorry that you feel you wasted resources and time skillbreaking ninjas. Fortunately those ninjas' skillbreaks are still usable even without the small bonus power they give. For the future I would recommend not committing to a system until it is actually released, as there are no guarantees as to how/what will be released. That should hopefully solve these issues moving forward.
Thanks and have a great day!