I have two slightly conflicting comments.

First, there is (or used to be) regional variation in this sort of interaction.
In small towns in the South or Southwest, the normal social expectation was that you have a little bit of friendly chit-chat with a shop-keeper or clerk prior to checkout even if you've never met and will never see each other again.
While trying such banter in the Northeast might earn you a glare or a suspicious stare thinking you are going to try to sell them something or recruit them to your cult.

That said, I have a complaint similar to yours about Taco Bell drive-throughs recently. (Yeah, I know. I really really shouldn't.) Now when you drive up, they ask "how are you doing?" not "what would you like?" What the heck? They can't even see me!
Even stranger than that, when you say, "I'm doing fine" there's a big pause before they think to say "what would you like to order?"

My social skills are at a loss here. What's the expected behavior?

Do people just ignore the "how's it going?" and immediately start ordering?

What's the point in delaying a long drive-through line of cars to make sure a stranger you can't even see is having an adequate day?
You know why I'm here. You know that I'm ready to order and quickly get away. That's why I'm at a fast food restaurant and still in my car.
If I had more time, wouldn't I be choosing a healthier option?