Currently, the health bars are a bit counterintuitive as the first half represents the health of the lowest armor segment, and the second half represents compartment health. Until the player understands the mechanics, this causes a sudden change in how tough it appears to be to damage the enemy for no apparent reason.
I suggest having separate bars with different colors (perhaps gray for armor and red/green for compartments), one above the other (either higher on the screen or overlapping).
Also, the health readout when targeting something with internal hp should display the health percentage of the lowest armor segment until it's zero, then switch to internal health.
The getVisibleDamage function needs to keep returning a combination of armor and internal health for compatibility though I guess.
The one issue I can think of with changing the health reading on the targeting HUD is armor repair devices. If a ship repairs its armor — such as the Ranx dreadnought with its patch spiders — that could cause a bit of bouncing back and forth between the two values (though I suppose that could also be a useful means of letting you know that you do have a self-repairing ship on your hands).