You can choose before playing if you want to use motion controls, so that's an improvement. Not sure if that mean those minigames just don't appear or the controls are changed, though.

Yeah that's seemingly how it works. They just don't show up. But I don't really get why you can't just use the pro controller cos as I say, none of them so far have used the joycon in a way which couldnt easily be done with the pro controller (or even buttons)