Long story short, Prey 2 is currently in the process of being overhauled by Arkane Studios after transferring hands from Human Head Studios. Kotaku has found several emails confirming as much, including the one credited to the outlet above, and believes that "Bethesda Misled Gamers" about it.
Now, I don't really care that a company denied to comment or deflected responses concerning its lineup of games in production. Not every project by studios should be presented to the public (and thereby their competitors) during its inception, but only when the developer is ready to do so. Every company, including Bethesda, should have the right to keep them secret, and it's not like they're hiding something illegal or devious like a war crime or something like that.
At any rate, it's good news that Prey 2, if that's what it's going to be called, is still in development, and that Arkane Studios is seemingly behind the wheel of the project. As a spiritual successor to System Shock 2, the game has incredible potential and Arkane Studios' experience with Dishonored and BioShock 2 puts them in good stead, regardless of all the rumors and DRAMS.
If anything, the best thing to come out of this is the phrase "press sneak fucks". I am a "ninja" after all.