That is curious. I was going to answer with the suggestion that the brake wheels were revised when the cars were given AB brakes... But, there are lots of photos of the prototype cars with late paint schemes, that still have the brakeshaft, and I didn't find any with a revised brakewheel location (and the brakeshaft was not necessarily revised when given AB brakes- some roads did, others not). And, I note, all the photos I can find on Bowser's site of their HO models show a brake staff, regardless of date of the paint scheme.
So, I think you have a good question there. Could it maybe have happened due to a change in Chinese factories? That was the explanation for a lot of production issues for several manufacturers 5 or 6 years ago. Might be worth an email to Bowser.