I think from the pilot, Terok Nor became DS9 because the Federation was asked by Bajor to help them rebuild from the occupation. It was mainly a humanitarian mission, and when Sisko discovered the wormhole the Federation actively sought to bring Bajor into the Federation because access to the wormhole was a huge strategic gain for the Federation.
Empok Nor was located in the Travis System and abandoned by the Cardassians. The Travis System was in Cardassian space, until their war with the Klingons. It looks like there was no real strategic value to that sector other than the proximity to Federation space. It had no value to the Dominions. Maybe during the first Cardassian-Federation war, they used the base as a station to launch attacks. The first introduction of the base identified that the Cardassians used it as a research station on psychotropic drugs, and probably did researched on weaponizing it. They probably chose the location because it kept research far away from main Cardassian space, and was far enough so they can deploy their psychotropic weapons on enemies.
Instead of repairing an abandoned station, filled with traps, and with systems that don't really match Federation technology, it would likely be faster to just build a brand new station from scratch. Towing that station would take years if they can't warp it to another sector. During the first season of DS9 there were several incidences where the station's hidden booby traps were activated, even after the Federation attempted to clear them all out.
Paul Weaver wrote:
Weren't the mines on Bajor mostly on the surface, maybe the odd moon.
Why ship raw ore up to the station to process when you could just build a processing plant on the surface and ship the refined product?
Currently in the US, there's a plan to build a giant multi-hundred mile long pipe line from Canada to Texas, called the Keystone pipeline, where it will carry crude shale oil to refineries in Texas. If you could explain why it would be better to just build refineries in Montana or some other border state with Canada instead of building the pipeline, then your very logical question about building ore processing plants on the surface on the world would make a lot more sense.
With that said, I think that there were ore processing plants on the surface of the planet, however certain raw ore types were probably brought up to the stations because they might be a specific rare type that required the station's energy output to process it. Additionally processing could further mean distribution of the processed ores to freighters, and they needed Bajorian slaves to short them.