After a duel with a gT KD in my new ship which is totally maxed with 6 missiles and two torps, I discovered I did no damage to his shields at all, even though I was sure I hit him. Afterwards, I did a quick test, asking him to hold still while I fired on him. Sure enough, no damage. Here's some screenies.
Launching full salvo of 2 nemesis/cataclysm/paralyzers with a torpedo duo. Time stamp included.
Status after the hit of the strike a couple seconds later. As you can see from the explosions, it was a direct hit and no damage was taken.
I'll be testing later if this is on all cap ships or just ones with Cruiser Shields. I didn't check, but I believe I could still hit his hull if his shields fell.