While the comic was being written, scientists were secretly working on the first A-bomb. To maintain the secrecy of the project, the Defense Department ordered DC Comics to pull the story. Yes, apparently, the Pentagon feared the Japanese might see the comic, go, "Holy shit what if that's a real thing?!" and then build anti-nuclear domes around all their cities. Or something.
This was, more or less, their line of thinking.
Now the government, being the government, didn't tell the folks at DC why specifically they wanted the comic pulled. For all DC knew, the comic was pulled because J. Robert Oppenheimer was secretly working on a Superman. They wouldn't even learn for another year that a real atomic bomb was being developed, and even then, the similarities between the real A-bomb and Luthor's weren't exactly obvious.
This was probably never a rough draft of the A-bomb.
It Gets Creepier:
We mentioned that DC Comics had no idea what it had done wrong ... and that's exactly why, a few months later, they did it again. An ongoing storyline in the Superman newspaper strip showed a skeptical physics professor blasting Superman with a cyclotron (a type of particle accelerator) to find out if he's really as invulnerable as he says.
"Man, we just used school funds to blast an alien full of our most powerful lasers; I'll give you the whole fucking university if you keep quiet about this."