This is what lists are for. They are type safe, but at the same time, they are resizable. There are a couple different types of lists, but in your case, the basic list should work well:

import System.Collections.Generic;

public var objScout1:GameObject;
public var objScout2:GameObject;
public var objScout3:GameObject;

public var wave1 = new List.<GameObject>();
//The GameObject between the brackets determines the type the list holds.

function Start () {

    wave1.Add(objScout1);
    wave1.Add(objScout2);
    wave1.Add(objScout3);

}

then you shouldn't have to change how your instantiate code works. You can access lists the same way as arrays with the index i.e. wave1[0].

And its easy to remove items:

 wave1.RemoveAt(i);

as described here.

Yes, there is a distinct difference between built-in arrays such as GameObject[] and Array(). If you want to resize a built-in array, you'll have to handle the removal of the element yourself using a custom method to rebuild the array. Here's code that should do the trick.

function RemoveItemFromArray(i : int) {
    var newCount : int = wave1.length - 1;
    if(!newCount) {
        wave1 = null;
    }
    else {
        var newWave : GameObject[] = new GameObject[newCount];
        var y : int = 0;
        for(var x : int = 0; x < wave1.length; x++) {
            if(x != i) {
            // Skip the element at index i
                newWave[y] = wave1[x];
                y++;
            }
        }
        wave1 = newWave;
    }
}