And if the underneath route isn’t there? If he breaks open on the deep ball down the field the QB is just not supposed to throw it even if no one else is open?

The concept is called with a deep route. Any route being run on a given play has potential to be the target if it is what’s open on the given play/how it is defended. If you don’t want to throw a deep ball under any circumstances, then you don’t have a deep route on the field. Doesn’t matter what the intention of the deep route is. What matters is how the play develops and what the progression is.

He was clearly open and had a step with a good opportunity to catch that ball. That makes it a good decision.