When you think about it, Replicant Yonah being stricken with the Black Scrawl doesn't make sense. It's revealed near the end of the game that Replicants suffer from the disease when their corresponding Gestalt either relapses or dies, and Gestalt Yonah was most certainly receiving the essence extracted from Gestalt Nier/The Shadowlord to keep her stable along with the others, which should have prevented any chance of Replicant Yonah from suffering the disease. Presumably, it might be because the treatment stopped working after a millennia of being a disembodied spirit, forcing both Replicant and Gestalt Nier's hands with their respective Yonahs' well-being on the line, but it's never explained.
The fact that the original Yonah became a Gestalt very shortly before the original Nier might explain it. All of the early Gestalts created before The Shadowlord immediately relapsed, including Yonah, and it doesn't seem like The Shadowlord's essence can reverse the process of a Gestalt relapsing when it's already underway. If it was possible, the Black Scrawl wouldn't be incurable, and there would probably be a lot less relapsed Gestalts running around. It's likely that The Shadowlord's essence just slows down the process and that this gave the people running Project Gestalt enough time to put her in stasis.
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, whose 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.
The remake's ending E makes this explicit when the administrators are talking to Kaine.
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 Kainé 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 Kainé 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 has Kainé turn into a true human meaning there's no worry of her Gestalt relapsing, but according to the Drama CDs, Ending C is probably the kinder ending if you actually care about her. Following Nier's sacrifice, Kainé 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.
However the short story canonically called Ending E, "The Lost World" given by Grimoire Nier, a book published exclusively in Japan (and fan translated), does have Nier and Kainé meet in the Forest of Myth a few months after Ending D of the game.
The official Ending E in the remake does have Kainé recover Nier through sheer force of the Power of Love and the magic of the Forest of Myth.
One entry in the Apocalyptic Log loading screen is "I can hear sounds". Drakengard's final boss in the E path is introduced by "I. Hear. A. Sound." This hints that the Queen Grotesquerie was responsible for whatever happened in Nier's world.
Certain Shades in-game carry items like used coloring books and old schoolbooks. Now, why would they be carrying those? Well, what kind of person usually uses schoolbooks and coloring books? Children. And those Shades are rather small... isn't it possible that those Shades are the Gestalts of children?
In the fight against Goose in the ballroom, Kainé responds to Goose's statement that they shall never be forgiven with "We don't want your forgiveness". The implication is that due to Tyrann, she can understand Shades. She has always been able to understand them. Even the ones who don't want to fight or who were only defending their homes. Kainé could have simply stopped and translated, and so much bloodshed could have been avoided. However, Tyrann made her into a blood knight who didn't even care.
It's made very clear in all branches past the first one that the ball-shaped shades are babies. This is the same shade type Hook belches at you and Kainé during its boss fight, the implication being that he at some point swallowed actual babies just to use them as ammo, and Mother Goose was not present during that time to even attempt to save them.
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 NieR itself!
The weapons from Drakengard being available in the game makes sense as well. When Caim and Angelus entered Nier's world, they brought those weapons with them, and those weapons were eventually lost as time went on. Until Nier finds some of them.
The DLC weapons also count. Their description reveals some references to Caim.
A somewhat meta one, but Yoko Taro has stated that the game was inspired by the World Trade Center attacks on September 11th, 2001, in that the attacks made him realize that anyone can commit acts of great evil if they believe they are in the right. Nier's birthday in-game is revealed in one of Yonah's letters as being September 11th.
given by Grimoire Nier, a book published exclusively in Japan (and fan translated), does have Nier and Kainé meet in the Forest of Myth a few months after Ending D of the game.