When I engage in combat and take physical damage to my ship (armor damage) the visual effects of a damaged hull does not go away when using an armor repairer. The armor repairs, but the graphical effect of the damage remains. This does not correct itself until I jump into another system through a gate. It may resolve itself by docking, but I never tried that.
Also, even when you do not repair it I notice it does not reflect the actual amount of damage sustained. For example, I had less than 10% armor remaining after a particular battle, but my ship barely showed any damage. I could not see the full extent visually until I jumped into another system.