Even the Ordon goats conceptually represents both cultures. Its circular horn seems to signify the unity of both, while its blue and white striped fur somewhat represents the patterns seen on Lon Lon Milk bottles. Furthermore the goat is a more sylvan species, and a fair replacement for the horses of Lon Lon as they are both hooved quadruped species. I'm not sure if all of this really holds up, but from a purely conceptual standpoint, it makes sense to me.
Also, since it is widely speculated that Ordon Village is built atop the abandoned Kokiri Forest (because of how geographically similar they are and how both sport treehouses), it all makes even more sense. I'll write up a little timeline:
- Link travels back from Termina and ages naturally.
- Link joins the Hyrule castle guard to protect the Hyrule Royal Family.
- As revealed in one of the Gossip Stones in OoT, Malon wishes to be swept up by a knight in shining armor, so Link happens to do so.
- The two wed and decide to resettle in Link's home, the Kokiri Forest. Perhaps the Kokiri still existed at this time and helped the two settle in, along with any other settlers (like Talon and Ingo).
- Over time, the Kokiri leave the forest, as their job—as the forest spirits under the Deku Tree's command—is over. In the Adult Timeline, their job was to provide a home for the Hero of Time to grow up in so he could topple Ganondorf. In the Child Timeline, perhaps their role was to provide a home for Link and his following generations, and as they take new forms (monkeys), they'll continue to watch over and assist them.
- Link and Malon start the Hero of Time's bloodline.