So that answers the question about the government not putting 2 and 2 together?
Dodge the entire 2nd part of the point with the farm the Smallville attack it's pretty clear that anyone with common sense would realize Clark is Superman. There is suspense of belief in the CBM world and there is bad writing. This is bad lazy writing.
This is a poorly thought out criticism and shows how people are willing to just rant on and on about a perceived flaw without ever thinking through their objection. Hilariously, you started down this unbidden. Nothing in this thread would lead someone to post on this, but some nudge caused you to say, "I'm going to irrationally rant on some perceived MOS failing now and by gum, I'm going to stick by it like it matters!"
What?
Think it through for a half-second longer than it took you to decide to post a poorly conceived criticism. Our hero found a journalist secreted away in a secure location without the support of an intelligence network. He took down an otherwise undetectable surveillance drone and delivered it to the unpublished location of a high-ranking military official in real-time. He's obviously able to gather information on American secrets seemingly at will. He's capable of traveling across the planet in under a minute and able to fell entire buildings with a mere look... but he's already cooperated on a joint mission with your forces and aligned his interests with yours.
You want to talk about secrets? Who do you think has more to lose if that exchange of publication if they push on an identity that's already their ally... compared to Superman releasing information about the government's indiscretions from black ops to the Suicide Squad? Cynically, it's clearly a case of Mutually Assured Destruction, except
not for Superman... he just moves to a country ready to welcome him with open arms, while the USA sits smoldering in the blowback for its secrets revealed. The US would have to be as short-sighted, half-cocked, and small-minded as the critic who raises this issue to
press the issue. Superman holds all the trump cards in this. It's completely reasonable for the government to either give up or not act upon the secret because there's literally no upside to it.
At best you get some leverage on someone who's
already on your side... at worst, you turn an asset into an enemy and make him an ally to another state. Proposing persistence in this is as crazy as saying you actively look for things to blackmail your friends and family with.