Never hurts to use everything at your disposal...depending on how the missile is guided, chaff or flares are worth a shot, when you consider the cost. Cheap as hell, maybe only 30% effective, but...never hurts to try!
point well taken, but if one is trying to stop a hypersonic cruise missile (or similar) there may be but seconds, or fractions of seconds, from the time CIWS is ineffective, and an impact.