Wouldn’t you say the second season was a take on bringing real world problems into Star Trek context? The dystopia reality is an authoritarian regime founded on racism, and the planet is dying from ignored climate change, only barely being held together by essentially giant force fields in the sky.
If anything I found it a bit too on the nose for Trek, though that impression might be colored by this being the first real life issue of my time that is a topic in Trek. When old Trek shows aired the first time I was just a little kid and missed most of those; so I can’t relate as much.
Interesting background knowledge that they were supposed to be gay, puts a lot of things into new perspective.
That being said, I don’t really like the idea, I enjoyed them as these unlikely but good platonic friends. I don’t think adding a romantic aspect to them would have improved their characters. For example Garak has many traits that could be interpreted as stereotypically gay, especially within the time period the show was produced. Him being a flamboyant and well spoken heterosexual works better to subvert cliches. Come to think of it, Bashir also isn’t the manliest of men. Which i also find more interesting for a heterosexual character.