I add some security against slash and grab crimes of opportunity by looping a cable lock that has loops on its ends, rather than a built in lock, around some fixed interior part of my car (in my case my trunk's hinge) and stick my u lock through the other end. This probably won't work with high quality thick cables.

As long as your cables aren't severely bent or suspending the bike I wouldn't be too worried about damage other than scratched paint. Also, you can probably avoid the issue by routing the rack's suports through a different part of your frame.