I think that Navi is a real fairy, But from a different clan (Race, if you refer to call it). There is three clans of fairies, and they are all run by the Queen Of Fairies that is found for powerups.
I think---
Nayru's Clan: the pink healing fairies. They're base is the Fairy Fountains, dotted here and there. They die after healing, and they can speak, but they normally have nothing to say.
Din's clan: Not seen on OOT, but these are Fighter fairies. They are rare to find, because they live below the ground in tunnels. The fairies in Din's clan are red, like Leaf on Phantom Hourglass.
Farore's clan: These live in the forest, and they do not have a base. you normally can see them following the Kokiri kids as partners. They are several colors, and Navi is one of them.
Names that are common on the clans:
Nayru's clan: Sirinu, Tatsuya, Spirit, Light.
Din's clan: Flame, Shadow, Blood, Night, Blade.
Farore's clan: Navi, Celia, Sinibi, Lirt, Cherrina, Tatl.
Nayru's clan fairies:
Awaiting photo
Din's clan fairy:
Farore's clan fairies: