Kinda weird how 90s anime were more okay with flat-out saying "Yep, they're gay" (e.g. Sailor Moon, Cardcaptor Sakura, Utena) than later.
Though granted, the Utena manga was pretty bad when it came to straightwashing, and someone will bring up the Sailor Moon DiC dub if I don't
Utena's deal came about as a difference of vision between anime director Kunihiko Ikuhara and mangaka Chiho Saito. Ikuhara viewed the central relationship as romantic and Saito viewed it as a friendship (and likewise also just wrote completely differeng plots for Juri). The anime (and movie) interpretation is obviously what's stuck in population consciousness, especially in the anglosphere, but it is worth noting that the lack of wlw romance in the manga was a creator choice and not one foisted by a publisher or sponsor.
As for general trends, Japan, like much of the world, experienced backlash to LGBTQ reputation in media as creators pushed boundaries. Textual queerness in 90's anime was edgy, weird, and provocative, and also much rarer in broadcast anime compared to film or OVA releases, which were just the wild goddamn west in terms of content (notably, even the turboqueer Utena anime lacked a kiss or a romantic I love you between the leads - you needed the theatrical film for that).
Moving into the 00s and 10s, you had some backslash against that. Kid-targeted series like Pretty Cure could allow for cutesy homoromanticism, but were designed to play it too safe to ever indulge in "edgy" content, while more teen and adult shows could happily acknowledge that gay people exist for a joke or fanservice without ever pursuing anything but predictable heteronormative relationships in their text.
Yes, I am old enough to have been a Haruhi fan, why do you ask.
As anime became more homogenized between a handful of production companies and sponsors, you started to see comparatively fewer "edgy queer" stories without LGBTQ narratives ever really being pushed into the mainstream in their place until relatively recently- and even stories that do put queer characters and relationships front and center have to fight an uphill battle against the soulless forces of marketing, as seen with my earlier complaints about Bandai's handling of Mobile Suit Gundam Witch from Mercury, or the fact that I'm In Love With The Villainess, the unapologetically turbolesbian originator of the "otome game isekai" light novel, is only getting an anime this season (go watch it though).
Entertainment history is messy and doesn't move in straight lines of social justice, is what I'm saying here.