I believe it would have to have been discovered by accident (at least if the records/memories of the site have been blanked) ... as an active site would have been revealed during the Dominion War - either by the Vorta maximizing efficiency, or by others feeling the war qualifies as the great evil for which this installation was built.
And if the bombardment only exposed some of the power conduits, then there might not be an immediate identification with the device/site ... only later, as someone traces the lines, would the location become apparent.
Bob