I don’t have any hard knowledge here. USB 3 provides more current when needed so it’s power supplies have to be a little better. That may lower VBUS noise a little. You are correct that noise over the USB cable from a USB 3 source isn’t affected by the potential extra speed, but if you have a USB 3 hub doing other things between the PC and the DS you might have more noise. I have a 10 port USB 3 hub with (among other things) five USB drives with my music library. I don’t hear the results of electrical noise from the data reads of the USB drives in the DS, but I do see just a little more noise on the scope.
One thing that I always liked to do is to put a powered USB 2.0 hub right before the DS with the DS being the only device on it. That can lower noise along that path to the DS and simple USB 2.0 hubs are cheap.