"Heavy armour piercing missile. Effective against ship hull."
The hull damage from this missile is mitigated by Armor, so to inflict maximum damage you should avoid targeting a heavily armored room.
The small amount of system damage done by this missile can trigger a significant repair response from the opponents AI. This effect can be far more disruptive than the actual system damage, as it may prevent them from repairing/buffing other rooms.
Using the Engine in combination with evenly placed Armor across your rooms is an effective counter to ships that rely on the Penetrator Missile as a primary damage dealer.