Kotaku has obtained an internal email sent by Arkane creative director Ralph Colantonio from May of this year declaring that the Austin studio would be making Prey 2, and it would be a totally new thing, and also "spiritual successor to System Shock 3." If that's a typo, it's Colantonio's and not mine.
This news comes after Colantonio told Rock Paper Shotgun, in a piece published yesterday, that he has no idea why anyone would think that.
Kotaku also obtained a second email from Colantionio, sent after the rumors began, telling employees to to not talk to the "press sneak fucks" who asked questions.
So why the cover up? I honestly don't care enough to speculate. The major publishers love to hide things. Oh well.