"I just wanted to know that IF/WHETHER you were gay" sounds more natural though. Who tells you that 'were' means it's not true anymore? Do tell this from the cases like 'If I were you'. In this sentence things are happened in the past, I wantED to know that you WERE, so actually we rarely say I wantED to know they ARE, which means I don't know if they are gay right now, this is outta the question. We are talking about things you wantED to know.

I think it just depends on the context of the conversation. It is correct if you are talking about someone who was gay in the past, but is not anymore, but if you are talking about someone who is still gay, then you would use are. Both are correct I think. ^.^

You are correct. Were is past tense so it means they used to be gay. Are is present tense which means they still are gay.