I believe armor is applied for each ship though. So say you have 100 ships with 10,000 armor and 1,000 health. HBC has 8,000 Armor Piercing. The first ship's armor blocks 2,000 damage (10,000 Armor - 8,000 AP) and then it takes 1,000 damage and dies. The beam now has 3,000 less damage and continues on to its next target. But I can't confirm that since it is fairly hard to test.