I mean dude flat out admits to having a torture fetish, and on multiple occasions tortures Snake or the man he was cloned from. Combine that with that line in MGS1 and the kiss in MGS4 and it's safe to say there was something there.
I always thought it was a love and respect kind of thing. Not literally romance. The way you'd love a another person that brings out the best in you competitively. And respect them for being who they are.
I dunno though, I guess it could be gay? I don't think it'd bother anybody, but I never took it as romantic love kind of shit.