Kojima has had a history of strange representation and writing with regards to LGBT characters and ideas. I mean, his tweet here is a good example:
In general, despite Kojima being a weirdo on his own terms, a lot of his views do still stink of traditional Japanese value systems. Japan is not actually that positive towards sexual minorities, despite its... comparatively progressive stance towards transgender topics. This isn't to say that Japan is great with these issues either, though.
As a gay person who generally loves Kojima's work, there are definitely aspects to his personification of queer individuals that rubs me the wrong way even as he frequently at least attempts to subvert gender norms with his characters. This, however, feels like a result of trying to create unique, different characters and juxtapose otherness with his wacky-yet-serious plotlines. I don't think the intent, unfortunately, is to portray LGBTQ characters positively.
It's a bummer. I'm hoping he gets better. Especially now that he's good friends with Del Toro. I think he's evolved at least a bit from his Snatcher and Policenauts days... but he's still got a ways to go.