A simple method to use without a lot of mission testing, go into the lab - turn transparency on.
Aha, I think this is possibly due to the normals on the faces facing inward on most faces. I guess collision only apply for the direction normals face.
Anyway, here is a list of ships that show this problem in the lab (I am assuming proper behavior is slightly see-through, not all or nothing on some faces)
GTF Apollo
GTF Angel
GTFr Chronos (Chronos #medical does not show this problem)
Terran Probe
Nameplate area of unnamed GTD Orion
GTD Polaris Extension
GTD Polaris Pylon
PVF Anubis
PVDr Jackal
PVFr Bast
PVI Karnak
Karnak Reactor (and #cargo)
PVI Shah Extension
PVI Shah Pylon
Vasudan NavBuoy (and #destructible)
SF Scorpion
SF Gorgon
SD Demon (and #scan)
Missiles:
EVERY SINGLE MISSLE MODEL except for:
Barracuda
All Shivan missiles (incl. #Shivan variants)
Type One
Shrapnel
S_Cluster