Paint can dramatically affect the tone of a bass, either positively or negatively. I would NEVER strip paint off a bass I'm happy with tone-wise!
For example, I had my white Stingray Classic painted up with a fancy custom Marty Bell 3 color sparkle design. It was painted twice due to an error. I would be willing to bet the original white and first sparkle job are still under the current paint, meaning it's got 3 times the normal paint on it. But anyways, it mellowed the Stingray considerably. It actually sounds more like a vintage ray, a little less zingy which is fine with me.