Epona is named after the horse goddesses, yes.
But it's been confirmed that Link was named that because he's supposed to "Link" you to the character/game.

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Bomber's Notebook | Secrets of the Minish Cap Library | Theorizing Resources | Aralith's OoT Retelling
Voted as Best Zelda Theorist in the Summer '08 Awards. Thank you to all who voted, and to all who inspired me along the way!