*Oh, I found where the HH calls the idea that the Hero's Shade is the HoT just a theory. Pg.179, under 'Ancient Hero'.

It states that some theorize he is the Hero of Time. That isn't the same as calling it just a theory. And in actuality, HH states the Hero's Shade being the Hero of Time as a fact on pg. 118.

Ancient Hero

The ghost of the hero who teaches Link his secrets. Some theorize that the fact that he holds his sword in his left hand indicates he is actually Link from Ocarina of Time. - Hyrule Historia, pg. 179

Link, the Descendent of the Hero of Time

When Link steps into the Twilight, the crest of the Triforce of Courage on the back of his hand begins to glow, and he is transformed into a beast. When he regains his human form, he finds himself wearing the green garb of the Hero. The spirit of Link’s ancestor, the Hero of Time, teaches him his secrets. Ever since returning to the Child Era, the swordsman has lamented the fact that he was not remembered as a hero. This is the reason he passes down the proof of his courage and his secret techniques to the Link of this era, addressing him as “son.” - Hyrule Historia, pg. 118