Idk, I highly doubt that they don't know, and if they do, they probably don't care, they just go along with it. I've always called her a she, I've never really cared about the whole debate thing. To be honest, I thought she was a she from the start XD I didn't know she was pretending to be a dude until that one chapter XD I know though that the translator says they translate it as "he" as a matter of personal preference, I think they said the raws were unclear anyway.
I get where you're coming from with Urie. I assumed he knew, since he called Mutsuki a hypocrite that one chapter when he was being a little prick like usual. If they do know, like you said, they probably don't care that much. And lol, I thought she was a he from the beginning. After I found out about the whole wanting to live as a guy, I just started referring to him by male pronouns. Idk, seems kinda offensive to me if I just started calling her she all of a sudden :/