Except they haven’t.
This all started when SpoilerTV found some Vimeo casting videos via the Supergirl Wiki and 4Chan, and in them the Supergirl and Jimmy Olson hopefuls have a conversation mentioning Superman. The problem with people believing this is proof of Superman in the series is that casting sides for this sort of audition process rarely has any real story details, for the very reason that they don’t want them leaking out like this and spoiling everyone.
A big recent example of this is The Force Awakens. When they were looking to cast Finn and Rey they had casting sides for a “Thomas” and “Rachel”. These used dialog and settings from The Hunger Games. Using the logic these people are with Supergirl, that would mean that Episode VII replicates a scene from Hunger Games…when we all know that obviously isn’t the case.
Could Superman be mentioned in the Supergirl series? Of course. But using casting sides as “proof” of that is just reaching. And if I remember correctly they’ve said that Kara would be the focus of the series, not her more-famous cousin. That means there could be a “Superman Returns” style MIA Kal-El in the show…