You'll find more information on an actual Soul forum. This is a car-recommending section of a website, unless you are looking for a new car. Your car seems fixable. I would take off the rack yourself and see if that's the problem. Get someone else in the car and drive on a bumpy road. That person can move around the car and see where the sound is coming from.
Post your same problem here:
If you are looking for a new car go for a Honda Fit. That car is small on the outside but huge on the inside just like a Soul