I've felt that John has known about MC & Nicole from the beginning. A scheming/blackmailing/rapist/asshole successful businessman really doesn't have his own home bugged with cameras, etc?? At the very least to insure the people he literally fucks over don't track him down to try the same. I figure he's calling him son because he has seen how the MC manipulated Nicole to his own needs, just as John would. Plus you have to figure John has been doing this to people for decades, like the MC is his only bastard son running around??
I think John was expecting the MC to arrive back home that night, to exact his revenge on the MC's mom...would make some sense the weird way the father was trying to tell him something after he found out the MC wasn't going to make it home. Probably has a special surprise planned for Nicole as well.
Edit: to be fair, the Dev probably won't take that much of a dark turn in the story, but it's something very realistic given what we know about John so far...we shall see.