Link watched this entire exchange intently. And he quite willingly sat on the ground when asked. "I've heard stories of gods and goddesses not getting along, and those ones were family. I figure if family can't get along, there's no way gods and goddesses from other worlds would get along."

Luckily, Link was fairly used to being sniffed, thanks in a large part to Skullkid. Link knew he had a distinctive scent, based on that conversation, but, had no way to know the particulars. He suspected he reeked of magic, especially with a third of the Triforce affixed to his soul. It was possible that there was a faint scent of the three (or....four) goddesses, based on that as well. And he was someone who spent a fair amount of time around shadow magic, for some reason.

On a more mundane level, Link was a fairly clean kid, who obviously spent a lot of time outdoors, and around animals.