If just one nuke were discovered, imagine the general din and excitement in Congress, not to mention in every Mayor's and Governor's office in the country. They can sneak one nuke, maybe, but if they try 20 and even one is discovered, we'll hear about it.
I'm not so sure, if 1 plane had hit the WTC, I bet it would've been called an accident. Of course, that's saying it was the only one hijacked, they couldn't cover up 3 others as crashes.
I think a nuke discovered and stopped would be absolute top secret and the upper levels of government would go into bunkers. This stuff was all worked out long ago.