There are a number of these checkpoints on various freeways out of San Diego.

I think you're right - it's less about the information elicited from the question asked and more about the driver's response (both verbal and not verbal).

I have a friend who is a Hispanic American, born and raised in San Diego. She lives north of the checkpoint on the I-15 and therefore gets pulled over into secondary from time to time.

She tells me the questioning tends to go something like this:

Officer: "How are you doing tonight?"
Friend: "Fine" (with a slightly perturbed/quizzical/stressed look)

That's the end of the interrogation, and then the officer waves her through. I guess the word "fine" with a rushed demeanor is all it takes to convince someone of their status as somebody who's an American....