I understand where you come from. I promptly leave any battle once my shields are down.
But I have to conclude that the current implementation does make kind of sense - at least historically. I imagine the ships are modular in the same manner our regular warships are. So when a ship gets hit, there is a good chance the armour deflects the shell or at least protects the internals from the explosion. But the shell might get inside and the damage is then quite serious. Of course, you isolate the damaged area so your ship stays afloat but the internal compartment is pretty much destroyed.
And and imagine our guns would be accurate enough to be able to hit a specific location repeatedly. The armour at that location gets destroyed soon and you've got just a hole and open way to your internal. For the hull itself it's just a loss of few percents of its integrity it is a hole and 0 protection for whatever is behind that armour.
Also, fully engineered hulls usually can stand quite a beating, regular NPCs are not a good sample of hull toughness.
But again, I hear you, RES hunting Anacondas is just ridiculous.