I remember a discussion like that on the old forums. I think instead the healthpoints of the liquid metal armor could be the ship's power reserve for the armor, and if the power reserve for that section of the ship were down, the armor would be down for some time, for example if a lot of fire was concentrated on the armor covering the power reserves, the armor would lose power for a short time and allow the complete destruction of the ship. Kinda like tank armor, some different calibers can penetrate while calibers with penetration under the armor thickness would not pen. same for space combat, I guess. Better guns=more chance of penetration and also draws more from the power reserves. Obviously for bigger ships the fight is not over if the shield is down. They are made of an advanced futuristic alloy that could act as armor, but have a damage model. weapons resembling traditional cannons or machine guns (kinetic weapons) but carrying advanced ammo could be mounted to shred weak spots while armor is down.
Another way to do it is to add armor that acts like skin on knees, slam a shot into the armor, it heals with some power from the ship. This could bring up interesting situations where one section of the tiny armor plates is not healing, and you could easily send a missile into it.