The linked ending of OoX seems to suggest that Link is leaving Hyrule. It is of course possible that he goes on after OoX and then returns to Hyrule. The Historia might just not have included that:
It's the first option. The credits sequence in the linked ending shows Zelda on the balcony of what could only be Hyrule Castle. It cuts to a forest with Hyrule Castle in the background, then pans up to the sky where a complete Triforce is shown. Then it pans back down to Link waving goodbye to many people. It very highly suggests that the setting is now Hyrule. Then he is last seen sailing away.
This ending scene and the events surrounding it are mentioned next in the beginning of the LA Manual.
Though you fufilled the Hyrulian prophecy of the Legendary Hero and destroyed the evil tyrant Ganon, the land of Hyrule enjoyed only a precarious peace. "Who knows what threats may arise from Ganon's ashes?" the restless people murmured as they knitted their brows and shook their heads. Ever vigilant, you decided to journey away from Hyrule on a quest for enlightenment, in search of wisdom that would make you better able to withstand the next threat to your homeland.
So after OoX, Link arrives at an unknown destination for training.
Months of difficult travel passed. After a long and fruitful voyage, you breathed deeply the sea spray from the deck of the ship that carried you home to Hyrule.
Now Link is done training, and is returning to home Hyrule.
But your homecoming was not to be. Suddenly a squall struck your ship, and though you valiantly fought the waves, a lightning bolt reduced your ship to splinters. Your world faded to black as you sink into the darkness of the storm-tossed sea with the remains of your craft.
So he shipwrecks, then the next game, LA.
In a nutshell, following this game order, the most obvious course for Link should be:
ALttP/OoX/[Training]/LA
. . . And I'm surprised to see that the HH timeline agrees with this too!
I am still not sure if the "Master sword" in OoX is really THE Master Sword
It definitely isn't. How would it go from the pedestal in ALttP to a basement where an old man lives, still within the childhood of Link? That reminds me, there were four places where you could get the sword. (It was always the second of two upgrades available in either order, in both games)
So apparently Ganon of LoZ has no intelligence at all. Perhaps Link did not kill the mindless Ganon, but just merely defeats him. Or maybe Ganon's minions resurrect him with a sacrifice but like Twinrova, they only brought in a Ganon with little intelligence. This could explain why Ganon appeared in LoZ with no hint of resurrection after ALttP and OoX. It could explain why he was not really bright in LoZ as he just sits in his lair waiting for Link and gets killed by one silver arrow and a magical sword.
Interesting thought... But I really think he died there. I think when the source you quoted labels him, "devoid of any particular intelligence," it is just trying to justify the fact that his plans in LoZ aren't very convoluted like other games. It's comparing him to previous games where he was an evil mastermind; where he did have quite a bit of particular intelligence. He's not mindless in LoZ, he just doesn't have any diabolical plans this time around.
But from this we can infer that Ganon was still capable of human thought:
One day, the Great Demon King Ganon, who planned to rule the world with darkness and fear, led an evil army corps and invaded the kingdom and snatched the Triforce of Power.