GUI Text Problem

The issue is that the GUIText Component uses a special normalized coordinate system, meaning for it to show on the screen its x and y coordinates need to be between 0 and 1 (e.g. 0.5, 0.5 is the middle of the screen). Since you have attached it to the projectile, that is unlikely. Instead, put the GUIText in a separate GameObject that doesn't move. You will have to get a reference to that new object so you can tell the score to change, but there are several approaches to that (e.g. keep a reference, Find(), etc).

guiText is meaningful only if the object is a GUIText. Assigning the GUIText to the projectile makes it a child, what doesn't set the projectile's variable guiText.
Another problem: the variable lastCube exists in each projectile you instantiate; if you create a new projectile each time you shoot, lastCube will always start with the null value.
A simple way to make this work is to create a script for the GUIText (let's call it GuiScore.js), place the variables lastCube and Counter in it and declare them as static, so they can easily be accessed from the projectile script:

static var lastCube: GameObject; static var Counter: int = 0;

function Update(){ guiText.text = "Score : " +Counter; } Then change the projectile script to:

function OnCollisionEnter (myCollision : Collision) {
    if (myCollision.gameObject.name == "Cube" && myCollision.gameObject != GuiScore.lastCube){
        GuiScore.Counter++;
        GuiScore.lastCube = myCollision.gameObject;
    }
}