We have fitted roof boxes to many thousands of cars and have never experienced any issues with a shark fin antenna/aerial getting in the way. The roof bars will lift the box high enough so it clears the shark fin.
You can see some examples in these images and you can see lots more images on the roof box product pages on our website:
Husky 420 roof box on a BMW 1 series:
Hapro Trivor roof box on a VW Golf:
Kamei 510 on a Qashqai with a normal aerial that is flexible enough to accommodate the roof box:
Hapro Roady 350 on a Ford Fiesta, the standard aerial is flexible enough to fit under the roof box:
If your aerial won't bend and you are concerned just contact us letting us know the distance between your aerial and your roof bars and also which boxes you are interested in. A few photos would also be useful. We can then take a closer look into it for you.