To expand on the title: I have two NPCs and I want VATS to be able to target one, but not the other. Is it possible to set this up without scripting?

If I remember correctly, child races cannot be targeted in VATS, so you could create a duplicate race that has the "child" box ticked and assign it to your untargetable NPC.

Cipscis

Hmm...that may just work. Out of curiosity, why can't child races be targeted. What, specifically, prevents it and how else might I duplicate it?

Its hardcoded into the game engine as part of their whole 'killing children is bad and you cant do it!' thing. It was this way in Oblivion too. (Meaning they just had NO children in the game) You check that box, and the engine interprets that and doesnt let you targets them. One side effect is you may not be able to kill a 'child race' either. But I'm not sure.