Yea, during the assault on the AI HW it's quite possible to pass the "point of no return" where you
know the AI will kill you if it doesn't die from the current attack, so liberal use of warheads to destroy/disable/de-supply the AI becomes viable. Iirc in one game Faulty used
5 nukes during the end-assault, largely to deal with the incoming waves and such from the AI that simply couldn't be handled by the defenses. It bought him enough time to win.
In other words: they're great "this game's going to be over one way or another, soon" buttons
I also find judicious use of EMPs valuable when dealing with alarmingly-sized threatballs, but it's usually better to avoid the necessity.
And of course if you're playing the later stages of Fallen Spire you don't necessarily have to care about AIP (to a point), and opening major engagements with EMPs (and possibly lightnings) can become a commonplace and effective tactic. Even there nukes aren't a great idea until the end, though.