For submodels all the time, I can think of a few solutions.
Stretching while warping doesn't happen anymore in Galaxy charts.
The shield bubble size could be rectified with a few invisible polygons placed at the perimeter of the model (though I think BC makes the bubbles too big anyway, this is a nice way to control that!)
And the hardpoints could be assigned to the mainbody, and switched out when the wings change.
I don't have an answer for system damage, perhaps ghost the main hardpoint to the submodels when the HP is made, and write a script to copy the damage the submodel's HP recieves to the main HP?
The wings, or submodels would only need to be dumb ships with minimal HPs.
Forgive me if those have been thought of.
When Apollo was working on ATP: Dimensions (sheds a single tear), he mentioned that the same system would work for turrets. What has changed?