Plot hole: When Pacey and Joey get locked in the Big K-Mart, they run to the front doors and start banging on them and yelling at the guard. The guard, who is in the parking lot turns back towards his car and faces directly towards Joey and Pacey in the front windows. They aren't that far from the guard's car, and he was looking directly towards them. There is no way the guard would not have noticed two full-grown adults standing in the front glass doors pounding their hands on the glass and yelling at him.
Plot hole: When Pacey and Joey are in the break room, waiting for the police to call them back, they start arguing. The phone suddenly rings, and Joey asks Pacey not to answer it in order to finish their conversation. But this doesn't make logical sense; considering their desperate circumstances (being locked in the store all night) and how hard they tried to get hold of law enforcement to help them get out, there is no way Joey would not want to answer such a critical phone call. It may have been their only chance to communicate with help.
Answer: It's the same apartment Joey had in NYC. Comparing it to the beginning of the Finale; you can tell it's exactly the same location, furnishings, Plasma TV etc. Apparently Chris was only living with her at HER apartment, and now Pacey has taken his place at the end. I guess this implies Pacey successfully started his own restaurant business in NYC as he had dreamed, to be with Joey.