They don't.

Every single piece of food is unique. So no one knows exactly how much of anything is in anything.

They're pretty close though. They can control down to the gram level how much of anything is in any of their products, and they can usually be more accurate than that.

From there, they can look up the caloric contents of their ingredients and calculate roughly what the values are. And as with their food items, the exact caloric content of a particular ingredient isn't known, but we have a very good approximation for these things. It's not NASA accurate (you won't do the equivalent of hitting a small piece of moving rock with an even smaller chunk of metal from 23 million miles away), but it's accurate enough for you to figure out if you can have that third cookie and still hit your weight loss goals (you can't).