It doesn't actually made a difference if it does apply or not… it reduces the bonus from class vitality and NPCs don't have classes

That said, if you make the opposition easier to kill, then it just balances the two sides, so fights don't really become that much more dangerous.
My point is, in Cloak and Dagger, the fights are supposed to be fast and deadly because fights are supposed to be the last thing a player wants to get into. Yes, keeping the health levels of NPCs the same gives them a bigger edge, serving as further disincentive, but Vitality jumps up really fast on Special NPCs, so I don't think the players would be big fans of having to chop through a huge block of Vitality when ambushing a senator while he has a greater chance of fending them off because their Vitality is so much smaller than normal.