|Copyright DC COMICS|
I think it was JOHN BYRNE - way back in the mid-1980s when he (and others) revised SUPERMAN's origins in the wake of the CRISIS On INFINITE EARTHS series - who first posed the question as to why anyone would ever suspect that Supes might have a secret identity. Sure, it was traditional for masked heroes (and villains) to have other identities - that's why they wore masks to conceal who they really were - but KAL-EL didn't wear a mask, so why would anyone suppose he might be hiding who he really was - or even that there was a 'really was' to hide?
However, Byrne's version of Supes was never a vigilante, so let's just allow, for the sake of discussion, that no one would have any reason to imagine he had another identity. First though, I'm not convinced we're on solid ground going down that route, because if he didn't disguise himself in his 'off' hours, his neighbours would've been bound to cash-in on the fact by selling their story - "We're Superman's Next Door Neighbours!" - with photos of him sitting out in his back garden in a tee-shirt and jeans. But let's pretend otherwise. Let's just accept that no one ever looked at Superman and thought that he might become someone else when he hung up his cloak at the end of the day, or wondered about where he lived and what he did when he wasn't catching criminals. (And to be fair, it wouldn't have occurred to them on his first few public appearances - but eventually they'd have started to wonder.)
However, that's not how the whole Lois suspecting Supes being Clark came about. It was the reverse of that - she looked at Clark and realised that he bore a resemblance to Superman - and that he was never around when Supes was (and vice versa). Well, you can't have one without the other, obviously, because if Clark is Superman then the reverse is also true.
What about SUPERBOY then, when he was retroactively fitted in to Clark's continuity and history? Surely no one had any reason to suspect him of being other than who he was? Au contraire. People knew he must live in SMALLVILLE, but not precisely where - and they also knew that they'd never seen him attend school in his costume (or any other outfit). He surely had to have a disguise then, and was hiding amongst them. To me, it seems the most natural assumption in the world for them to make - within the confines of a comic designed for kids.