DestroyImmediate or Destroy are static functions and you have to provide a reference to the object you want to destroy. GetComponent on the other side is not a static function. It requires an instance of a GameObject or a Component on which it searchs for the component.

If you call GetComponent within a MonoBehaviour script it will search on the GameObject this script is attached to (it's the same as this.Getcomponent()).

        if(go == null)
        {
            var goA = GameObject.Find(i + "a");
            var goB = GameObject.Find(i + "b");
            DestroyImmediate(goA.GetComponent (Waypoint));
            DestroyImmediate(goB.GetComponent (Waypoint));
        }
        else
        {
            DestroyImmediate(go.GetComponent (Waypoint));
            DestroyImmediate(go.GetComponent (WaypointDual));
        }

Also keep in mind that DestroyImmediate ONLY works in the editor. Never use it ingame! Same rule applies the other way round: Don't use Destroy in an editor-script.

You should actually use a true editor script like this (not tested i'm a C# guy :D):

// UnityScript (JavaScript)
class DestroyWaypoints extends Editor
{
    @MenuItem ("MyMenu/DestroyWaypoints")
    static function DestroyWPs () 
    {
        for(var i:int = 0; i < 105; i+=1)
        {
            var go = GameObject.Find(i+"");
            if(go == null)
            {
                var goA = GameObject.Find(i + "a");
                var goB = GameObject.Find(i + "b");
                DestroyImmediate(goA.GetComponent (Waypoint));
                DestroyImmediate(goB.GetComponent (Waypoint));
            }
            else
            {
                DestroyImmediate(go.GetComponent (Waypoint));
                DestroyImmediate(go.GetComponent (WaypointDual));
            }
            Debug.Log("Waypoint on Object "+i+" or "+i+" a|b should be destroyed...");
        }
    }
}

btw if you just want to delete all Waypoint and WaypointDual scripts just do it that way:

var allWaypoints = FindObjectsOfType(Waypoint);
for(var Obj in allWaypoints)
    DestroyImmediate(Obj);

var allWaypointDuals = FindObjectsOfType(WaypointDual);
for(var Obj in allWaypointDuals)
    DestroyImmediate(Obj);