Also LGBT NPCs totally need to happen regardless.
We already have those.
Most of NPCs are people Cloud and Co. interact with in a fairly casual way. For myself, I am rarely if ever aware of the sexual orientation of people I interact with casually on a day to day basis. I'm not even 100% sure of the sexual orientation of all the people I work with (nor do I ever spend much time wondering about it. I don't just assume that because someone is with a partner of the opposite sex, they must be straight. They could be bi.).
Anyway - For all we know, the game is already full of LGBT people whose sexual orientation just didn't happen to arise in the brief course of their interaction with Cloud. Like, what about those two Shinra guards down in the corner of the Sector 7 pillar? They could easily be partners.
That said, would it hurt to turn the two lovers on the train into two men or two women? Maybe it would - because then people might assume that the reason they killed themselves was because of homophobia. That would certainly be world-building, but perhaps not the kind of world-building we want.
I'm just trying to think of existing NPCs who could be made explicitly LGBT without either sending a problematic message (like Mukki and co) or, as Octo said, sticking out like a sore thumb.
Of course, with the wonderful graphics now available it would always be possible to show figures in a crowd holding hands, making out etc...