ANY object between the antenna and the satellite will degrade the signal to some degree. Different substances will have different levels of effect.
There is no "correct" answer to whether it will provide "bad" reception. It might, it might not. Depends on which way your car is pointing at the moment, what you have loaded into the box, etc., etc., etc.
Make sure the antenna is as far away from the box as possible. Otherwise, you just have to live with it.
One other thought - you don't leave the roof box on all the time, do you? Hopefully, you remove it for normal use, and only have it on for trips.