Maybe. But I do not think so.
My experience is that it does not seem to have any impact on the fish.
I am trying to breed PJ cardinals (maybe Banggais later on) and I have around 20.
Also have Yellow tangs, chromis, fiji damsels (blue w/ yellow belly & tail), saddleback, cinnamon, maroon and ocellaris clowns, sleeper goby, mandarin, lawnmower blennys and scooter dragonettes.
So far no wierd behavior.
No babies from the PJ cardinals yet. (only 4 are old enough to anyways.) When the PJ cardinals or clownfish pairs start having babies, I would be confident saying there is no side effect of the dual light cycle.