According to a Famitsu interview with Taro, via
Siliconera, the developers have yet to make this final secret public as it “would definitely be bad.”
‘“That” has yet to be found. Since the developers feel that it would definitely be bad, they have yet to make it public. Due to various circumstances, this something made its way into the game. Since they feel that going into any further detail might cause some problems, they won’t say more about it. Think of it as NieR: Automata’s last secret.’
In addition to that, Taro also mentioned that he already has plans for his next game, and that it would be nice to have something to announce on NieR’s 10th anniversary in 2020. Considering how successful the game has been for Square Enix, we can certainly expect to see more of this quirky franchise in the future.