I'd think a color change to anything other than white on a 65 Shelby (except maybe some original race cars), would hurt the value.
Other years, it depends, like has been mentioned. Any concours level car with a color change should be a hit on value though. If anyone would want to show it, almost impossible to recover the points deduction to earn a Gold award. I don't think SAAC even allows known color change cars in concours anymore.