One thing I wonder is if the Squad simply thought revealing his secret identity wouldn't be a big deal. Their feeling may have been Superman's friends would just accept the fact, and if it were revealed to the world, the bulk of humanity would probably not care.
I think I have that comic. From memory, Superman becomes quite upset at what he thinks is betrayal, but then he makes a deduction that they are all imposters because each android has given itself away, eg. Batman had not grown any beard despite not shaving that morning. (Is that the one? I think it is...)
Anyway, you hit the nail on the head, dmat. Baddies just cannot believe Clark Kent is all that important to Superman. The writers touched on this occasionally through the Silver Age. Which baddie could imagine Clark is a real person, and one half of the Man of Steel, and of vital importance to their enemy? Most enemies of Superman would naturally assume the Man of Steel could and would establish a new secret identity quite easily, or even, perhaps, that he has many secret identities.
We know different. (Or, at least I do.) The loss of Kent as a secret identity would be devastating for Superman. Or maybe the loss of the Superman secret identity would be devastating for Kent. Whichever.