Warning first theory:
Now as all good Zelda fans know there are three goddesses who created the world of Hyrule. This is Din the goddess of Earth or fire who created the earth. Then there is Farore who created Hylian life, and she is associated with wind. The third Goddess is Nayru creator of the world's physical laws. Now in Wind Waker there are two sages: Medli Sage of Earth awakened with the Earth God's Lyric and Makar Sage of Wind and awakened with the Wind God's Aria. Now the Earth God=Din and the Wind God=Farore so aren't we missing a sage for Nayru. Now I must point out similarities between the awakenings of Makar and Medli and the revelation of Tetra as Zelda.
YouTube - The Legend of Zelda Wind Waker: Tetra's Identity Part 2 YouTube - Medli awakened as Sage Legend of Zelda WindWaker Wind Waker
(Sorry I couldn't find one for Makar)
Now all three are revealed to be someone of importance by their ancestor. Fado revealed Makar as the Wind Sage. Laruto revealed Medli as the Earth Sage. And Daphnes Nohansen Hyrule revealed Tetra as Princess Zelda. A more subtle element to Zelda's awakening is the presence of Zelda's Lullaby in the background. The Wind God's Aria and Earth God's Lyric were also present in the scenes where Medli and Makar were awakened. Now we all know that Zelda is one of the seven OOT sages. She is the Sage of Time. Now wouldn't time go under the category of Hyrule's physical laws. So I believe that when Tetra was revealed to be Zelda, the mantle of a Sage of Time fell to her. KDNH was probably likewise the Sage of Time as the bloodline of the Time sage is within the royal family. Though the name of the apparent "Awakening song" doesn't match the theme of the other two, I'd like to point out that Zelda's Lullaby is unlikely to be the Song's actual name. That song seems to have always been the symbol of the Hyrule royal family before OOT Zelda was born. Therefore I believe that the song's true name is "The Time God's Lullaby." What do you think?