I don’t think Rubio “got clobbered”, but it wasn’t exactly a shining moment for him either. Paraphrased, the question was, “What part of the nuclear triad do you consider to be the most important?” No one - including Rubio - actually answered the question.
You are right. But it is a stupid question, offered by a would be poseur. Obviously, all three parts are important. But the question was intended to show that the questioner was more hip to insider terminology. That is the tactic of a poseur, trying to strut how "with it" he is, rather than actually communicate an idea to those listening.
It did not hurt Trump in the slightest. Those who really understand the psychological aspects, involved, will immediately see the point. It was the way not to ask a question, if you wanted a serious answer.