Where is it shown that Din and Farore have male mortal forms? I haven't played the Oracle games to know if the characters who share names with the goddesses are supposed to in fact be them, but they were all female there.
However, we do have incarnations or representative forms of the goddesses in the form of spirits, quite a few times in the series. While they're their own characters and probably not the goddesses themselves, the dragons in Skyward Sword are likely the closest thing to those three goddesses being reincarnated--possibly like how Zelda in that game was Hylia in essence. And Lanayru and Eldin were indeed male in that case. I don't really know if they would quite literally procreate, as I would imagine reproduction of the divine would be a more spiritual type of reproduction and not literal/physical birth.
Zelda is a human, born from humans, but she's descended from a reincarnation of Hylia, so in some way, she is still a descendant of a goddess. I don't really think Majora would have a connection to Hyrule's divinity, simply because he's not from Hyrule, as far as I know.