Following the events of "Empok Nor", would it not have made sense for the Federation to take control of Empok Nor and make it into a Federation starbase a la Deep Space Nine?
Not really. DS9 was a pretty unique situation, where the inhabitants of the planet that owned the station asking the Federation for help operating it. Starfleet had a decent amount of peace time to pour resources into the station to fix most of the problems, but fixing Empok Nor would be a waste of military resources when it was obvious that the Dominion War was right around the corner. Not only that, but operating two
ex-Cardassian stations meant that they'd be dependent on their soon-to-be adversaries for parts that they couldn't make themselves.
That said, I could see them trying to do that in the post-war period, but it might be easier to build an all-new starbase than refit something built by people whose cities and industries were blasted to rubble.