The entire damage system is fubar. I've had 100% shields and hull, mk XII MACOs sometimes, MkXI KHG others. One time a 2d green beam type animation briefly connected my ship to the gate and I died a heartbeat later. I barely saw in a split second my shields dropped then I died.
I looked up the damage stats and aside from a couple of minor 100-dmg from nearby spheres, I had taken no damage from the gate other than a single plasma torp of 60k crit range. It registered entirely to hull, none to shields. The damage is instant, the graphics don't even correspond to the damage you get. I NEVER took any damage in the logs to shields, but it instantly applied entirely to me and killed me.
The entire NPC damage application system is fubar and snafu to the extreme. It doesn't work along any logical pattern and it doesn't even adhere to internal coding restrictions. It just rolls the dice and kills you. Then it thinks of some after-the-fact weak-ass justification for why you died. It doesn't even have to match whatever graphical representation of the weapons hitting you.