I wonder if there was some thinking in higher circles that 1999 was too iconic a year to be used for such pessimism, that it might be subliminally bad for their audiences/profits?

I'm trying to think of 1999 set apocalyptic sci fi and drawing a blank. Or even much else. I've yet to see Class of 1999 myself, or even '84 actually, surprisingly. Strange Days was set in 1999 but was future noir, otherwise, hmmm... Probably more cyberpunk than anything else. I think cyberpunk probably put paid to a lot of economy fails/computers/machines go mad Y2K musings at more than a more or less self parody level 'cause it was all hip hacker VR anti Establishment business. Economy's for squares and killer toasters or whatever are just old hat kind of thing.

Maybe horror was ok 'cause it's already negative, and sci fi is "more" about action and hope? I'm just guessing, but it seemed like there was a little late 90's/early 00's religious/apocalyptic horror boom with End of Days, Stigmata, Bless The Child, Lost Souls, The Exorcist re-release and probably some others I forgot.

End of Days was kind of a weird, awkward film right? It's been ages but I remember the drama/horror thriller/action mix just not gelling, and Arnie just not fitting in with almost anything. Gabriel Byrne being badass and some goofy fun though.

Was Maggie any good? I heard mixed things and then kinda forgot about it.

That list has some promising looking films. I especially like the look of Omega Cop, with the mighty tagline :

"The year is 1999
John Travis is the toughest cop alive
... He is the only cop alive"