Yes, killing does drop morale.
Ironicly, the AI always attack mission-critical buildings, but leave certain others alone (Residences, Nurseries, Universities, and Agridomes).
Nukes are a kill-all element at the end of the tech tree in many RTSs. Short answer, no, I wouldn't want a nuke in OP3.
Long answer; Where the heck are they going to get their plutonium and refine it? The advanced labs?
it takes a lot to build an A-bomb, and in a place where the only thing separating you from instant death is a wall and a pressurized environment, there are better ways to kill enemy colonists than drying to drop a massive nuclear device on them.
That is, if you're the sadistic sort who attacks the colonists simply for the hell of it.
And I'm half certain that the Enlightened Leaders of Earth didn't include nuclear weaponry in the 'encrypted military files' for the MAD reason. The only way I can think of their inclusion would be if the colonists faced some kind of evil alien menace out to extinguish mankind.