I have not looked at your capx but if i undersrtand what your saying then try this:
Global var BombCounter[0]
Global var BombHP[1] // only needs 1 hit
Global var BombTimer[1.0] // add a timer for the bomb so you can increase the timer as the difficulty increases <img src="smileys/smiley1.gif" border="0" align="middle" />
System.onStartOfLayout
-> System.setVale(BombCounter[0]) // this will benefit you later when you want to restart the game.
system.Every[BombTimer]Seconds
-> System.CreateObject([Bomb], random(WindowWidth), -10)) // create a bomb at a random x position, and a y of - 10 so we dont see it spawn
/* Im not sure how your destroying the bombs but i'll pretend there with bullets or something similar */
Mouse.onClick[Left]
-> System.createObject([Bullet], Mouse.X, Mouse.Y)
Bullet.OnCollisionWithObject[Bomb]
-> System.addTo(BombCounter[1])
-> System.addTo(BombHP[1])
-> Bullet.Destroy
System.CompareVariable(BombHP > 1)
-> Bomb.Destroy
System.CompareVariable(BombCounter > 3)
-> System.setValue(BombCounter[0]) // set it to 0 so we can count again
-> System.SetValue(BombTimer[BombTimer - 0.2) // increase the speed the bombs spawn at
Note, This was rushed and straight out of my head, If you need a example capx let me know