let's be serious, realistically Niki would know. It's either willful ignorance or Chika levels of cope.
I'd wager it's more that she's testing to which extent she can control him and Ami with the illusion of them having to hide it from her. "would they stop with me living here?", "would they stop if I got to know the other girls? (invite over events)", "would I actually be able to turn Ami's head around?".
Obviously that was all pointless, as what the conversation with Ami showed her (when she asks if Ami is having sex with him for real, long before she came along).
Regardless, I think Selebus wrote himself into a corner there, as he's done many times over, because Niki can't really act in a decisive manner because the rest of the plot has to catch up before it - meaning that she has to stay the oblivious mama Niki that lives with Akira and Ami until we've dealt with a lot of other stuff. It was the same with Chika, she couldn't discover everything that was obvious before the plot reached the point of fixing it with a TSS.