Good question!
The vacant one could actually be worth more depending on what the market rents are. It could be the one rented is in a long term lease below market rate.
All things being equal if the empty one is in like kind condition it should be worth just as much and could still sell for more just because an owner / user can buy and will pay the most. But if you can rent it for the same amount per foot as the occupied one then its worth the same but some people will put some value on an already occupied property. The difference would be probably a few months rent since it will take a months to rent it.