A strong low frequency shudder as opposed to a squeal is bending all the parts over quite a cycle of travel. For the long term health of the metal as well as comfort to the rider I know that I'd want to correct it. Also the shudder is being reflected into the contact patch on the ground. I don't see how a strong shudder can do anything but hurt the maximum reachable friction coeffienct. So likely your maximum attainable braking rate is suffering as well.