The way I see it, she is a totally different horse. Technically, this horse doesn't even need to be Epona, as you can name her whatever you like. Or since Link is a rancher, he has heard stories from people in the village who have heard about Lon Lon Ranch. Perhaps Malon, as Link marrying Malon makes the most sense, as he is brought up in a farming village.
Well, I simply try not to think about these things, it makes my head hurt. :3