So, I did some tests in 3.6.10b2 with all of the current files available.
GTF Ares: The middle of the "V" on the tail fins (flat exterior facing side, Left and Right side) shrouding the engines and the very tips. They are enclosed in the shield mesh, but still take damage.
GTF Loki: Left Side Pylon, Top-Front-Outside Corner. Shield mesh clips through this corner, exposing that portion, but I was unable to commit any damage.
GTB Ursa: Very bottom of the thrusters. Shield mesh clips through (helps to force engine subsystem off to find it precisely). This does expose the model to receiving damage in the exposed areas, but shots do not carry any further through the model. Both the inside and outside side of the thruster are affected.
GTB Medusa: Same problem as the Ursa, though to a lesser extent. Ship does take damage.
GTB Boaengers: No hole per-se and I could not cause any damage, but the Left Barrel's flat face (as you sit in the cockpit) is just barely protruding through the shield mesh.
GTS Hygeia: This thing might as well not have shields at all. They all seem to sit at the surface layer and just about every shot leveled at the ship (no matter how light the weapon) will cause damage. More spots than I can count.
Test Mission: Wanderers "Terran Parade" mission.
Exes Used: 3.6.9 and 3.6.10 by Turey's installer, every XT Build and every build posted since March 1st.
Test Weapon: 1/2 Power Subach HL-7
Test TBM: Every Ship had the following set by -shp.TBM: $Shield Regeneration Rate: 2.00
Screenshots: Yes.
I also noticed a disturbing # of ships begin drifting as I shot them, but I didn't track all of them or their rate of movement in relation to the number of shots delivered.
Next batch: Shivans and then Vasudans.