The racks certainly contribute to noise on the highway.
Most of the noise you get from certain road surfaces is the tyres. A different brand and tread pattern will change this characteristic.
Whilst some vibration may come from the diesel as Dazz says, any other vibration through the steering wheel is definitely not wheel alignment. It is wheel balance (front). Unless it only vibrates when you have your foot on the brake. Then it's a warped brake rotor.
If your rear tyres are out of balance, you'll feel it through the seat of your pants.