Should good brake pads be replaced when warped rotors are replaced?

If I was doing the repair, I would, as most likely you will have braking issues if you just replace the rotors. The rotors should have been replaced or machined the last time the brakes were replaced if they have warped already. Pads aren't expensive, and since you're in there to replace the rotors, it makes sense to put in new pads. The old pads are adjusted to the old surface, and may not work as well.

Ryans93 is right. However, it may be possible to scuff the pads if they have not been on for long.

Weighing in - I agree with the scuffing of the pads IF they are still at 8mm + in thickness. Below that, it's better to be proactive and replace them.