I've had this same issue with my iPhone 6S Plus and CarPlay after updating to iOS 10! The Apple Maps no longer automatically switch to Night Mode while using navigation after sunset! The screen in my car is now so blindingly bright that I can't use Apple Maps safely for navigation at night. I have a 2017 Hyundai Elantra that has the tech package upgrade that included a stock touchscreen radio that supports Apple CarPlay. It worked perfectly fine before I updated my iPhone to iOS 10!
Note that we are not talking about the new feature Night Shift, that is working perfectly fine. We are talking about Night Mode in Apple Maps that should change the interface to dark blue and black automatically at sunset while using navigation. It works on the iPhone itself still, but not through Apple CarPlay after the iOS 10 update!
This needs to be fixed soon, please push an update for this Apple!