Intelligence can be effectively suppressed, it depends on your environment. Clark grew up on a farm in a small town, not much chance his intellect would be challenged or nurtured there. Plus the crash landing could have scrambled his brain like with Goku.

And MoS seems to treat Clark's vulnerability with more insight and understanding of the human condition, of being an outsider and wanting to belong and be normal. The original Superman movies made him a bumbling idiot and then straight pussy. A 6'4" 225lb man who is used to kicking ass wouldn't suddenly not be able to defend himself again some drunk at a diner.