Why did Hyrule flood? Was it the Gods, as Wind Waker claims, or was it something more?
After Link defeated Ganon/Ganondorf in Ocarina of Time, he was given the choice to either stay as an adult or go back to enjoy his childhood. If he decided to go back to his childhood, he would eventually go to Termina. Because Termina is a parallel universe to Hyrule, the Gods had created an exact replica of Link just in case Ganon was to return, as if they had no idea where Link was.
This brings up another question. Are there different gods in Termina? One could assume that after Link left Hyrule, he was brought out of the Gods' reach. If so, this explains why the Triforce wasn't depicted or spoken about in any way.
The Terminian gods may actually be the four giants. Although they appear to be in an eternal slumber, waiting to be asked forth in using their godly might, the giants are considered to be guardians (not deities); however, they have been told to have created the world.
However, if one considers the term deity, it may bring to mind the form of which Link takes from wearing the Fierce Deity's Mask. The physical attributes Link acquires in this state could only be put as that of a god's. He gains a huge stature, tribal markings, an enchanted sword, and near-invincibility.
The reason you would think he was too powerful is that the mask is only able to be worn during boss fights. The only way to counter this is to perform a glitch or enter a Gameshark cheat that allows you to wear it outside battle. When these requirements have been met, you can easily compare the drastic changes in the green hero's size to that of a normal Terminian.
On the opposite side of the spectrum, you have Majora. Was the beast from which the mask was carved considered a demonic being? All the factors explaining his malevolent personality point toward this.
The mask was sealed for eternity after being carved because of its extraordinary powers. At the end of the game, the Happy Mask Salesman gets his mask back, but its power is apparently drained. After this, he vanishes out of sight forever.
Now, take a look at Wind Waker. It's based several hundred years after the events of Ocarina of Time. The prologue explains that the hero had saved Hyrule from darkness and left Hyrule in peace. However, it then details an evil coming back to Hyrule, for which the hero didn't appear.
Maybe this hero was too busy somewhere else. Maybe he was in Termina. This could support the theory of Link returning back to his childhood and visiting Termina soon after, leaving Hyrule off-guard to dark forces.
But what exactly are these dark forces? One theory claims that the Happy Mask Salesman went back to Hyrule and used Majora's Mask to take over the kingdom.
From this brings an even more realistic idea. In the events of Majora's Mask, Link has to stop the moon from crashing into Termina. If this were to happen again in Hyrule, what would be the consequences? Could the moon have smashed into Lake Hylia or a bigger body of water to create a flood? Or was it someone else...someone who wanted to gain revenge for meeting his terrible fate? Someone who drowned?