When I'm listening to my Metalcore and the breakdown kicks in (usually have a ****load of bass), EVERYTHING rattles. Bad. Dont even get me started on the trunk. I have the stock Shaker 1000, but still has a bunch of bass to it.
But no, it wont affect your paint, I have never heard of such a thing.. All it will do is rattle/shake the hell out of your windows and mirrors. I remember one time, my mirror was shaking so bad there was a car behind me that I thought was a Mustang. To my surprise, it was a Pontiac XD
The trunk rattling is common if you have subs in the back of your trunk.
It wont affect performance, exterior (except the trunk rattling), interior (except your mirrors and etc. rattling), or anything else. You'll be fine, dont worry.