I haven't used a clay bar on my custom paint streetrod but I don't think it would hurt it at all. 18k miles and I don't have any swirls or polish scratches. I wash the car a couple times a week and after any long cruise plus it waxed about every 2 weeks.
Now my dualliy is another story. It gets filthy dirty on the highway and after washing I use the claybar about twice a year. The clay bar does wonders for it. the truck is black and 11 yr old and it looks new after the clay bar rub.