As others have said the Cardassian trashed it before they left, so they left a few torpedeos behind. The Shield generators might have been considered a primary system and they had done some repair work on them. But lets examine the situation, the Cardassian had stripped Bajor of most of it's resources before deciding dealing with the Bajoran insurgence was more trouble than it was worth.
So basically we have a "back-water" planet, that has little to nothing of value. So why would Starfleet see the need to rush repairs on the torpedeo banks etc.. It's not like they expect it to see combat aytime soon.