I'm guessing you're referring to this line?
"Long ago, when Hyrule was still one country, a great King was said to have used the Triforce to maintain order in Hyrule."
Now, I suppose you're reading "used the Triforce" as "used the whole Triforce." But that's an assumption on your part.
OoT says that Ganondorf "obtained the Triforce" from the Temple of Light and "with the Triforce's power" transformed Hyrule into a world of darkness. So clearly Ganondorf "used the Triforce" to take over Hyrule, just as the king of Hyrule "used the Triforce" to maintain order in Hyrule.
So you have no compelling evidence that the king of Hyrule possessed all three parts of the Triforce to begin with.
Also, your reference to
missing parts is the result of an error on Nintendo of America's part when translating the
AoL manual.
The line reads, in Japanese,
「王子はそのたりないものを求めて、ありとあらゆる所を捜したが、なかなかみつからなかたった 。」
which translates to,
"The prince sought
for what he did not have, and searched everywhere, but he couldn't seem to find it."
The implication that the two missing Triforces were "what he did not have" was introduced by Nintendo of America and is not present in the Japanese script, which only says that the prince lacks "what he did not have."
Also, the scroll never specifies who wrote it, not in the English script and not in the Japanese, thus the identity of the person who hid the Triforce of Courage is a mystery. Since the game never specifies what part(s) of the Triforce were inherited by the prince, it could just as well have been the prince who hid it.*
*The scroll actually never specifies that its writer even had the full Triforce. In the NoA translation it reads, "I have left Power and Wisdom in the kingdom," but the Japanese only says that Power and Wisdom remain in the kingdom, without the implication that the writer ever possessed them.