Don't get me wrong, I weep a bit whenever I see a quality/collectible/historically significant stock with an aftermarket pad installed, but strictly speaking they are functional. My arthritic shoulder would welcome a pad on a .30/06 I intended to fire all day in a match.

If indeed the example you are describing is in otherwise excellent original condition, I should think the pad would knock 25-30% minimum off its value, to me anyway.