as far as the true hidden meaning, i dont know.
but i can tell you what it is supposed to represent in the game lore. which might help you figure the rest out.
i would decode the hidden meaning to be something along the lines of polytheism.
the exact lore of this series of games changes slightly from one episode to the next so my explanation will be more inline with the original episodes in the series.
the npc's in the game all believed in 3 gods, the god of wisdom, the god of power, and the god of courage.
these 3 gods each represent one of the 3 triangles in the 'triforce' symbol.
the god of wisdom is incarnated onto earth as the princess zelda, immortal though herself unaware she is anything other then a regular princess.
the god of power is always evil, seeking power for powers sake, he incarnates as a dark wizard who tries to kidnap the princess seeking to acquire the power of the triforce for himself. he wants all 3 elements of it in his possession/use. not just the one that is his to start with.
the third part of the triforce which is courage is incarnated onto earth as your character named 'Link' you play as this character who himself is unaware of his destiny until it plays out in the storyline as you play through the games. your goal is merely to defeat the 'power' character and rescue the 'wisdom' character and restore balance and peace to the land.
being immortal there is no way to permanently defeat the 'power' character so in each game it is merely sealed away for a time only to return in the next game.
i think the idea behind all this is just to get kids to stop thinking of a God, and instead think of gods plural.
maybe theres more to it then that, i dont know
the most sinister messaging in all of the games occurs in the episode titled 'twilight princess' in this one your character 'link' is transformed against his will into a wolf who is ridden like a horse against his will by a demon who is rebelling against a demon lord. thats the gist of it. they even have a snake god in this episode which is one of the 'Light Spirits which are guardian deities' so the idea that a snake little g god could be benevolent is one of the messaging that occurs in that episode.