At the moment (as far as I know), there are only 4 items that can be used against NPCs. I have some artifacts I would rather use against NPCs since I am not into PvP. They include but are not limited to:

Krionite Torpedo (Blast the enemy ship with Krionite Phase Gas vaporizing all shield energy on the ship)
Quantum Flare (reducing their chance of doing criticals assuming they have the chance)
Dark Pyramid (increases our chance of doing criticals assuming we can do them on NPCs)
Unstable Wormhole Emitter (warp away a NPC)

A Krionite Torpedo would be extremely poweful in this situation (possibly eliminating 3/4 of their HP as in Rouge Science Leage ships) but because the artifact already is limited by mission completion, this could be ok.

Quantum Flares I don't know how you can implement this when they don't have a scan score. As you would be using it for nothing but lowering their chance of a critical, I would rather keep it for hacking.

Dark Pyramids you use on yourself, so they provide their bonus regardless of if the opponent is PC or NPC.

Your idea for Unstable Wormhole Emitters has already been suggested in another thread.

This is something I'm not sure about. Do they not have scanning or is it just not shown? I assume it is there and influencing their attacks, we're just not seeing it. As someone who doesn't PvP, it would give me the chance to use it rather than just scrapping it.

And you're right, I didn't mean Dark Pyramid, I meant Positron Clouder which reduces their cloaking.