They (The Dark Ones) no longer moved him, so he stopped writing about them.
From this article on reddit:
So I looked him up and found this interview on diezukunft.de, a German website – Glukhovsky speaks German fluently (along with English, French, Hebrew, Spanish and of course Russian). I’ll translate some of the juicier quotes. For example, when asked about his stance on Science Fiction, Glukhovsky answers: “For me, Science Fiction is a tool to express things that move me. However, out there are a lot of Science Fiction fans who only want to read adventure novels. That is understandable when you think about the fact that not all, but some of them are teenagers who want an adrenaline kick.”
There’s also the whole issue of the monsters. I’m not spoiling very much (it’s mentioned in the first chapter) when I say that in Metro 2035, there are no monsters. Or, as Glukhovsky puts it, “this novel is about humans. […] He [Artjom] gets to meet a few mutants, but those aren’t the monsters.”
And a summary sentence from the author:
With that out of the way, how does this explain the sudden changes of Metro 2035? Well, the Dark Ones were a topic that moved Glukhovsky back in 2002, a topic that has stopped moving him now.
There is more, as well as a link to the interview (If you speak/read German, thanks to @TheLethalCarrot for the link).