It's depressing being always super-negative about it and these stories clearly also are a bit of escapism, but just my personal preferences - I also find it a bit annoying if they completely ignore homophobia as if it didn't at all exist, especially in a country like Japan. So a gentle reminder like this (it's not exactly looking as if it's going to be a huge subplot that'll take ages to resolve) that even if things are going well for those two not all is well in the world is I think appropriate.
I agree, I knew about my students if they were socially anxious, had to work, what their hobbies were, who their friends were, etc. but which among them might have been gay ... not so much. Just not discussed, except by the really advanced, more progressive students.
Then again, the teasing that goes on, some things come out between the lines.