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He can leave Zora's Domain you know. He probably went somewhere, found some cows, and was like "Oooo what's that? I think I'll eat it."

He's obviously swallowed lots of things. A few of those things being creatures. Also, to be literal, it's a dungeon, so it needs to have those things in it. As for the size issue... It's Nintendo 64, what more can you expect?