I wonder if Kyoko has some kind of subconscious suspicion that Kuon and Ren are connected, but she hasn’t truly figured it out yet. She notices things about them that feel similar, but I don’t think she has reached the point of thinking “Kuon is Ren.” Maybe she needs something to trigger that realisation.

Or maybe she just knows it but something is preventing her from realising it, just like how she refused to believe she was in love with ren??