While I agree with more or less everything else you said, I don't think civilian ships would really suffer tbh. Any ship that's large enough to have escape pods, should give players inside that ship a realistic chance to use those escape pods, otherwise they're just decoration. So even the civilian ships will become more durable compared to what they are now, although the military ships will probably become comparatively more durable.
And the way that ships get destroyed would probably change as well, like, some would basically not get fully destroyed at all. Fully disabled and posing no threat in ship-to-ship combat, sure. But take something like caterpillar for example. It's long, and all the critical components are on one end. You could probably blow up every component you can think off, and few of those cargo-compartments could still be perfectly intact. Which would probably be desirable for someone planning to steal that cargo, but it could also mean that even after all that destruction, you'll find couple angry crewmen with railguns and SMGs laying in ambush among the cargo.
Now, would the ship not getting fully destroyed solve the issue with decorative escape pods? Not really. Escape pods are supposed to save your life, not serve as a fun alternative way to exit the ship. If you can just stick around the ship and nothing bad will happen, then you don't need those escape pods. Ideally it'd be something like, the ship is mostly gone but has like 10-20% of fight left in it when you can choose to either evacuate or fight to the last. So those 10-20% should then cover such span of time as it takes for the crew to exit their stations and get to the escape pods, in lancer exiting the pilot seat, going through the door, getting on the escapepodbeds and then launching the pod would probably take like 20-30 seconds. Currently in 1v1 it takes far less time than that to just blow up a perfectly fine freelancer, 12-19 seconds on a Cutlass black (assuming you hit. But once you start hitting it, it's gone.). So I would see the TTK of a lancer go up quite a bit as well. However, ships that have military armor probably benefit disproportionally more.