Sort of what I was thinking, yes.
You'd fire at a ship system, and if you hit it that system would be degraded. Say, WBs, Torpedoes and LBs would lose a point of strength, lances would gain a +1 modifier to their dice rolls, thrusters would add 5cm to your turn distance, main engines lose 5cm of speed, with multiple damage to a system being cumulative.
The crew would repair this damage as they struggle to keep the ship in the fight.
'Critical Hits' could cause permanent systems damage, armour degradation, crew deaths, and (in extreme cases) loss of the ship itself.
In general, a ship would become 'crippled' by losing its ability to stay in the fight, rather than by being destroyed outright or losing an arbitrary number of hitpoints. As you mentioned, this makes more sense from a 'these ships are incredibly old and have survived innumerable battles' vibe.