Ugh, I'm sorry, I still don't get it.
Are you saying that the damage spreads the same regardless of whether there is armor or not? You need at least WH 16 missile to reach internal components of ships with armor level 3 (with a single strike)?
If a ship with 3 layers of armor (and no damage) is hit by a WH 9-15 missile, there will be armor damage on all three layers of armor, but no internal damage:
The same ship, getting hit by a WH 16 missile, will take internal damage:
Repeated damage (not hits, the damage) in the same area will, as far as I know, "fall" straight down through the holes to intact armor:
And here's an animated version of JacenHan's image, hopefully it makes it clear how the damage increases:
Album link: imgur.com/a/aaxKhlt