I would say that in the 1960s, when Mort Weisinger launched the letter column (he was one of the first editors to do so), there were lots of questions about the internal logic and readers themselves were encouraged to come up with their own explanations. This is probably why the mythology became so convoluted because they kept having to introduce new ideas that would answer those questions.

I'm not a fan of the stories where someone one day looks at Clark Kent and says, "Hey that guy could be Superman." I prefer to think that the people just don't see them as alike--there might be all kinds of distinguishing micro-details which we don't detect in comic book art, but which the characters pick up on, that tell them they are very different guys. Yet once a story says someone sees the resemblance it breaks that convention.

However, the publisher had to pump out hundreds of stories every month, on tight deadlines, on a small budget, to sell comic books that had cheap price tags and only made a significant profit when sold in bulk. So the secret identity dilemma was an easy plot and hard to resist.

But people don't thimk Clark is Superboy, because there's so much proof of the opposite. He has robots that fill in for him all the time. There are friends of his that will sub in for Clark or Superboy. He has super-powers that allow him to be in several places almost at the same time. And every time that someone thinks that they've proven Clark is Superboy, they are made to look stupid when it's shown that this could not possibly be the case.