I'm working on modeling an underlying superstructure for one of my old non-FS cruiser designs (known only as "Simple Cruiser 2")
Here's a WIP shot:

The idea is for a bunch of 'layers' of destructible subsystems:
1. In the holes of the superstructure goes the plating/armor -- fairly thin layers of metal-looking stuff which can be blasted off fairly easily. These would be pof'd as destructible subsystems.
2. Beneath them there might be lighter bracing/scaffolding. Depending on what panel was blown off, some of this might 'cling' to the panel (possibly as subsystem debris), and thus would just leave that panel empty. There might also be some deeper-in paneling in some parts of the ship, which would be under both the scaffolding layer and the plating/armor layer.
3. Under that is the internals; greebly stuff. Ideally a lot of it would be destructible and would have -destroyed submodels as well. Pipes that could be blown open, fuel tanks... some of these more advanced features might require scripting, however. Also, not all of the parts in this layer would necessarily be destructible; some of them would probably go together (pof-wise) with layer 4.
4. The superstructure will basically be indestructible. Until the ship is destroyed, it remains intact.
As for ship debris (once the ship finally explodes), I'm not entirely sure how that would be done.