If the store is empty, they won't mind. Actually they won't mind even if you eat your order and sit there with empty cups but its basic courtesy to give up the table if someone else is looking for place to sit.
I once spent 4hrs in starbucks planning our college fest with friends and they didn't mind
Yup. You would often find people sitting there for hours with their laptops connected to a power outlet. There used to be free wifi not sure if it still exists and what the limits are. It is better for them to have some occupancy than having an empty restaurant.