Thanks to background information presented in the game and in the Grimoire Nier, we know that the only force holding most of the Gestalts that still maintained their own identity has been the Shadowlord, who's existence acts as a stabilizing factor. The Shadowlord (Nier's Gestalt) was specifically created to keep all other Gestalts from lapsing into Shades and forgetting who they were. And since Nier destroys the Shadowlord, this means that all Gestalts will now lapse into Shades.
Replicants can only live if their Gestalts haven't relapsed yet. Yonah has the Black Scrawl (and always will no matter how many Replicants of her are made) because her Gestalt wasn't stable when placed into stasis.
This also means that there are no happy endings in this game.
If you get either ending A or B where Nier, Yonah and Kaine all live? Yonah will die soon anyhow because her Gestalt is now gone. Nier will likely die first though since his Gestalt was the Shadowlord and Kaine will follow once her own Gestalt has lapsed.
Ending C still means Nier and Yonah won't survive much longer, given that both of their Gestalts are now gone.
Ending D is much the same, though it make take a little longer for Kaine's Gestalt to lapse but Yonah is pretty much a goner.
According to the Drama CDs, Ending C is probably the kinder ending if you actually care about Kaine. Following Nier's sacrifice, Kaine is plagued by foggy memories of him. She cries whenever she sees a Lunar Tear and begins lusting after men who resemble Nier. And she can't understand why any of this is happening to her. The strain is shown in one particular Drama CD track to be breaking her down mentally.
One entry in the Apocalyptic Log loading screen is "I can hear sounds". Drakengard's final boss in the E path is introduced by "You. Hear. A. Sound." This hints that the Queen Grotesquerie was responsible for whatever happened in Nier's world.
This game is based on ending E of Drakengard, which required collecting every weapon in the game. This led many players to believe that collecting every weapon would have some relevance to the ending. We know now this was not the case. However, a lot of those weapons are available in the world of Nier. In a sense, the reward for collecting them is the availability in Nier!
The DLC weapons also count. Their description reveals some references to Caim.