I was thinking about the town secret, too. Problem that I stumbled upon was GD, the high amount of government interaction and the close proximity of the military. Not sure if it would have been healthy for Clark to be exposed to the entire town.
Just had another fun thought. Since Eureka wouldn't want to attract the press and the close military presence in the first place, Lois might be sent there to investigate strange occurrences with Clark trying to discourage her. And the townsfolk trying to hide all their less than ordinary equipment, and failing in the most obvious ways
Michael