After multiple perfect stacks of Chaos Swarm/Gemini combos seeming to have no effect on NPC Trident and Queen shields, I can only assume that this is a new bug.

sometimes this happens when the sector is buggy. Or historically with queens sometimes they have insane recharge rates which the devs have to fix (never seen that on tridents though).

As far as I know, the insane recharge rate is by design. You're supposed to kill off some of the smaller hive missions first.

This was first observed by me on a NPC Trident in a small skirmish in Deneb.

Have you noticed any other lag or anything while the NPC Trident's shields seemed impenetrable?

No unusual lag. While heavily active sectors sometimes lag, my Acer tab doesn't have as much lag issues as I've heard from others. After trying to dogfight a few proms and others I seem to be able to bring the shields down after a reload at the friendly dent. This was not neccesary before. Seemed odd to me.