Assume a default ship has a 100hp hull with the default armour (also called bulkheads, interchangeable name) taking 80% damage from thermal and 120% damage from kinetic. Upgrading to the Reinforced or Military versions will increase the hp of the ship, something like x2 for the top end (giving a 200hp hull) - but do not affect the damage reduction. Mirrored and Reactive versions will both increase the hp and shift the damage type resistance (mirrored is better vs thermal but worse vs kinetic, Reactive is the opposite). Those damage reduction values do apply to hits to modules as well (as illustrated in the OP) but as these don't change between lightweight/military hulls, the only direct damage reduction comes from mirrored/reactive. What the armour does affect is the penetration chance as the ship gets damaged.
Hull reinforcements behave in a similar way to reinforced/military armour - increasing the hp, so the military armoured ship with two +10% hull reinforcements would have 220hp.
So what exactly does this mean for penetration/damage to modules? When the hull is at full health there is no difference what armour/hull re-inforcements you have fitted. As the ship becomes damaged there are some differences though. Take the following two ships:
Well geared (Military + hull reinforcements): 220hp
Assume they've both been hit for 50 hull damage so far this fight. And are now being shot by a normal weapon:
Default: hull at 50/100 health, penetration chance: 60%
Well Geared: hull at 170/220 health, penetration chance: 49%
Further down the fight, they've both taken 95 hull damage and are again shot normally:
Default: hull at 5/100 health, penetration chance: 78%
Well Geared: hull at 125/220 health, penetration chance: 58%
So.. Better armour does affect module damage, but not in the way people often expect! I't something we're looking at as part of the loot/crafting update Michael mentioned in a recent dev update (along with several other combat balance issues), until then we've bigger fish to fry . There's several conflicting goals we're trying to juggle: To start with the question of randomised vs deterministic penetration - which is a highly subjective thing and from our investigation so far it tends to feel better for the attacker if deterministic, but better for the defender if it's slightly random. We also agree that changing armour should have a bigger effect on the damage your ship and modules take, but even the best armour should never protect them enough to make targeting modules a useless strategy. Not to say we're out of ideas, just nothing I want to commit to here .