There are many popular methods and what not people use to try and identify if the player is a guy or a girl. But the truth of the matter is there's no way to know for certain unless the person in question straight up tells you their gender... and even then, they could be trolling you.
I know a few female players who are actually into being skimpy with their female characters, so the idea of female players only play as female characters that are fully dressed or male characters to avoid being hit on is already debunked. I usually play as guy characters myself, but I'm not against the idea of playing as a female character every now and then, skimpy or not. I usually look to what type of character the said character is over how they look, and that's how I gravitate to them. This is of course null in a game like FFXIV where you simply MAKE your own character, but still, my point stands.
If the bonding system is a concern, the biggest thing you should keep in mind is that this is a videogame. It's not like you're committing to each other in real life. Me and a FC member of mine thought the same thing, so we went through with the bonding system. We're both guy players, but our characters happen to be male and female, so we said... "Why not?" Besides, I've used various in-game marriage systems, to the point of which I hardly even think about it anymore, let alone phase me in any way.
Long story short, does it matter? As long as you enjoy the company of that person, it shouldn't matter me thinks.
EDIT: I usually assume the other player is a guy until I'm told otherwise if I don't know the player's gender. Again, doesn't really matter to me though.
EDIT 2: Gay and Lesbian relationships exist in this world too you know. I don't know about you, but I'd rather not see this thread not go down that route like SO MANY OTHER THREADS DO.