Aw, come on Jim, I call bullshit on the whole Shadow Hearts thing.
Gay humor? Yes, low brown and childish - and I had some laughs.
Homophobic? Come on, was there actually anything discriminating? Was there ever anyone who said that being gay was wrong? Anastasia Romanov even thought it was "cute" when Joachim Valentine and The Great Question were doing some... things... after the battle of a hundred stages (it's left ambiguous what is really going on).
And what's with that "trying to have sex with any and all men"-shtick? They're chasing Yuri, they're only into Yuri. That's part of the joke. The fact that there's always a shop available, even in the darkest dungeon, because the two cartoony over-the-top flamboyant homosexuals are stalking the main character.
So, yeah, they use homosexuality in their humor. You can call it silly, you can call it low brow, you can call it childish - and if you're a snob, you can even call it insulting. But I do believe calling it homophobic just isn't really correct.
Now look what you've you've done, I've started ranting.