In the Supergirl pilot episode, Supergirl herself argues with a coworker about whether or not aliens exist.
But that wouldn't make sense if Superman is widely known to be an alien in the DC universe.
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Not enough is known about the super girl universe yet to know if Superman is regarded as an alien or not. We don't know if Super girl shares universe with Arrow or The Flash or the upcoming Atom series either. Superman if he exists might be considered meta human but in Arrow and the Flash super powered people are just coming into existence. The super girl pilot implies Superman is in active operation at the time.
In most medias, Superman is widely known to be alien as opposed to being a mutant or other type of super powered individual. Superman does not hide it and often shares the info to others about being alien.