I have ceramic coated headers on my regal and there is no way I would touch them, they still get hot. I think the ceramic coating retains more heat than no coating, but no exhaust header or manifold (unless it is water cooled like my big block boat manifolds) is cool enough to touch.
With that said, not using headers because of underhood temps robbing power is a waste. The increased flow of headers over manifolds far outperforms the increased underhood temp. The manifolds probably get just as hot, they just have less surface area to transfer it to the air. Also, headers cool down a lot quicker after you shut the car off than manifolds.
As for your paint on your hood, chances are that was the paint itself or the weather, not the headers, the timing was probably just a coincidence. I know people with headers on all sorts of vehicles and I have never had them fade the paint on the hood.