No it's confirmed. There is this technique called "getting crap past the radar" where you can't show explicit depictions of something so you give subtle (or not so subtle) hints instead. Hitomi is wearing a black turtle neck when she is sitting in bed with Usami and they start kissing. The next scene shows her in a white T-shirt.
There is no reason she would be in different clothes (while Usami is in the same clothes) after the transition except if she took them off for some reason. They 100% fucked. This is a classic example too where you show characters with different clothes immediately after a transition overnight. The original Sailor Moon anime had one where Usagi and Mamoru start kissing in his apartment and the next scene we see is Usagi sitting on the floor without her socks on. That's how ubiquitous it is. They've been using this sneaky shit for decades.
Everyone talking about if they had sex or not, but the real spice is the DEATH FLAG. "Nothing can separate us" You gotta be kidding me, that means he's got a terminal illness.