I read somewhere that anti-gay pushback gathered steam in the first half of the '00's (remember, the sodomy laws in 13 states didn't get repealed until 2003, and it was at the will of the USSC, not of the voters). Berman and his colleagues might have been nervous due to that. It is strange that TNG had "The Outcast", an unabashedly pro-LGBTQ episode, and DS9 had Dax's girl-on-girl kissing, and then Voyager and Enterprise had... nothing.
Honestly the mirror Kira, who was clearly bisexual, was hardly a triumph in LGBT representation, and probably fit into the same thinking that produced Jeri Ryan's wardrobe, if you get my drift. Earlier you had "Rejoined" which was a lovely episode where Terry Farrell and Susanna Thompson are intimate. It was very natural but short lived and forgettable amidst the story telling that happens in a given season.
Sigh This nonsense about "the television industry was still homophobic in the 1990s and that's why 90s Trek couldn't do gay characters" is exactly that - nonsense. Plenty of 90s shows had gay characters in them, among them Will and Grace, which featured a gay titular lead character, and that premiered in 1998, when DS9 was in its final season and Voyager in its fifth. There was definitely no reason there couldn't be any gay characters from that point on to when the Berman era ended in 2005. Hell, Enterprise's finale aired just one week before Doctor Who introduced its first LGBTQ+ main character.
I have to kindly disagree there. First of all, Sean Hayes' "Jack" on Will and Grace was a goofy caricature of gay men on a sitcom where life was rarely taken seriously. I would have to say that gay characters were rarely written, and even less portrayed in serious drams well through the end of Enterprise in 2005. Buffy the Vampire Slayer of course had Willow "come out" after moving to UPN, but that was after DS9/VOY had ended. Buffy also had a different demographic than Star Trek. The L Word premiered in 2004 and that was on premium cable. That show as one of the first I can recall that treated female gay relationships honestly.
Lastly, I'm not sure I would point to homophobia as the reason for the hesitancy, but you still had the "old boys club" in full effect in Hollywood. To be a writer/show runner, you mainly were a white guy who goofed off at an Ivy League school, and nepotism got you hired. Mutual backscratching was the name of the game. In this type of environment, how on earth could we expect LGBTQ stories and characters to treated with dignity? And as I said, you were dealing with a sheer lack of life experience there. It wasn't entirely that they didn't want to cover the subject matter, in many cases, they just weren't interested in it. Writers and producers are not cut from the same cloth as actors and directors, as they often do not study among artists.
I didn't say the TELEVISION INDUSTRY was homophobic. I said that CERTAIN VIEWERS were.
It was all about the advertisers. This was pre-Internet for the most part, when movements relied on newspaper coverage and mostly direct mail and phone calls to corporations and broadcasters.