Skull Kid can be explained as a species too. Same with other monsters.
Also, many species evolve or die out or something anyway, like the Kokiri to Korok, Gorons barely survived, and Zora evolved into Rito, at least during the WW storyline. Which makes BOTW funnier(though it has no official timeline placement) since it has both Zora and Rito, respectively.
But yeah, there's quite a few recurring characters without an explanation. Impa is a time traveler, which justifies her being anywhere(her body changes to fit the time, apparently, too. So it's not like she's always able to fight the same way, or fight at all). Tingle also appears in multiple timelines, which gets awkward. Same with his brothers. MM doesn't matter cause it's a different dimension, but WW has no ties to Four Swords at all. They're different timelines as is. Maybe he's an ageless being? He is from a different land(his origin story of Rosey Rupeeeland and all).