The naive (but potentially entirely sufficient) solution to this would be to make the score a static variable somewhere (so that all scripts can easily access it), and simply check whether the enemy health is <= 0 in the enemy's update function. If true, increase the score destroy the enemy's gameObject.

The more sophisticated solution would be event-driven. I posted a mini-tutorial that coud easily be adapted in this answer: http://answers.unity3d.com/questions/251765/invoking-all-instances-of-a-non-static-function.html

You can achieve that in more than a way.

As a first method, I assume that the only way an enemy can be destroied is through a collision with the player (or a projectile shooted by the player, I think you're making a FPS). So, you can attach something like this to the enemy (super-simple example):

function OnDestroy(){
   score++;
}

Obviously, this method will give at the player undeserved points, in case that the enemy dies after a collision with an obstacle on the scene, after the level completion...In other words, after a behaviour that doesn't have to give points. Rougly speaking, you have a poor control about points assignment.

Another, more controlled way, would be the assignment of points after a particular collision. An example:

function OnCollisionEnter (theCollision : Collision) {
   if (theCollision.gameObject.tag == "Ammo"){ //Ammo is just an example
      score++;
      Destroy(gameObject); //this will destroy the enemy!
   }
}

So, my advice is to implement something similar to this last method. Hope this helps!