Are they gay in the first two seasons? No, they're -nine-. Being absolutely bestest bestest friends forever in season 2 doesn't mean they're gay, just because they're too young to think like that.
That kind of reasoning is a lot more threadbare in Strikers. They're still BFF, but now they room with each other. In the same bed. (Not as a temporary arrangement, either!) They're closer to each other than to anybody else, period, including Fate's ostensible "kids". Again, the show never comes out and says "they're doing it", but either they're doing it, they have done it, or they will do it shortly.
(That doesn't make them lesbians, exactly, by Japanese standards; it's not clear that either of them have -rejected- the idea of dating guys. But of the two guys in the series with the potential to step in there, one of them is utterly ineffective even after ten years, and the other one is otherwise married...)