Counter battery only works if you know where to fire. If your first clue is they just launched their entire storage of missiles there is nothing to do. If you are fast enough maybe you can get the now-empty launcher, but modern military practice is shoot and scout so odds are against that.

Getting information on where things are stored is hard. It needs boots/spies on the ground (satellites can only get limited information and are easily fooled). As pointed out elsewhere, modern best practice is to not have a large warehouse that is easy to find and destroy, instead you scatter this stuff around in small units.