Can the POS refuse a sale when the shelf says an ingredient has run out?

No, and that is deliberate. A dish that you count runs out properly: at zero it greys out on the selling screen and sells out on your ordering page. But an ingredient going to zero does not stop anything. The sale goes through and the ingredient goes negative on Ingredients & suppliers. A customer is standing at the counter and the food is on the plate, so the sale really happened and refusing it would be the wrong answer. A negative number is a message that the shelf figure is wrong, and a stock-take is how you fix it. If you want a hard stop, count the dish itself on Menu → Inventory. That is how restaurant POS inventory management works here: dishes stop, ingredients report.