I had the same car damaged by two different hail storms, and one of them damaged our house roof (the car was at work the 2nd time it got hit).
I had the car fixed at a body shop the first time, the insurance premiums did not go up. The second time it got hailed on, it had lots of miles on it so we filed a claim and got a $1400 check from State Farm paying us for the reduced value of the car. Our insurance rates did not go up.
For the house, I had the State Farm adjustor look at the roof, selected a reputable roofer and had it fixed, and again, our insurance rates did not go up.
So, if I were you I would file the claim and either take the money or get it fixed.