The pantheon of Zelda is more akin to Norse and other pagan pantheons. In Norse, Greek, Egyptian, and other pagan beliefs, often there were multiple deities responsible for multiple aspects of nature.
So if we think of the Zelda pantheon like this we can make more sense of it.
THE MAJOR DEITIES
Din: Goddess of power, also associated with fire. Creator of the physical realm. Fire is also associated with passion, life and death, depending on if the fire is a forest fire, or used to cook and give light. Knowledge can also be a form of power as well.
Nayru: Goddess of wisdom and the laws of nature. She very associated with logic, order, law, knowledge, and because of this, can also extend as the goddess of mathematics, and the laws of physics.
Farore: Goddess of courage and valor, and the Earth and the creator of life. Because Earth goddesses in real life are also fertility goddesses, and since Farore is associated with the earth, being the giver of life, she can also be associated with fertility.
Hylia: I consider her to be the goddess of Hylians specifically. She is the embodiment of everything Hyruleans hold dear, and that is a perfect balance of the three virtues they hold most dear. That is, power, wisdom, and courage. She also doubles as a Messiah archetype, because she renounces her divinity to be reborn a human, suffers sacrifices and resurrections in order to help her charges.
THE MINOR DEITIES
Majora: Hear me out on this, if we consider Majora's Mask as a legend to explain eclipses, we can say that Majora is the deity of the sun, and the trickster deity. In most pantheons in real life, sun deities are often female, and in some pantheons, these deities can also double as the trickster gods. One of the best examples of a trickster is Loki. Often, Loki in Norse myth has some pranks that are nothing more than pranks, but sometimes his pranks escalate into something major, like the slaying of Baldur, which is the first sign of Ragnarok, the end of the world. In this sense, Majora's pranks in Majora's Mask started off relatively harmless and escalated in intensity to almost causing the apocalypse.
I also say that Majora is a sun god because the symbolism tied with it are often associated with the Sun. Not to mention its boss room has the mask come off a relief depicting the Sun, and is filled with color. As color doesn't exist without light, it doesn't get more symbolic than that.
Fierce Deity: God of the moon and the god of war. His direct counterpart would be Thor from Norse myth.
Goddess of Sand: Kind of self explanatory.
Goddess of Time: Exactly what it says on the tin
Goddess of Wind: Self explanatory.
You get the idea.
THE GUARDIAN DEITIES
Guardians in culture largely come from eastern religions, where there was a guardian god of everything. Like numerous rivers had a god. This also existed in western religions, though not on the level Japanese religions have. In Greek myth, scholars refer to this as personifications, in essence, the river itself was a deity.
They are
The Great Deku/Maku Tree
Jabu Jabu/Jabun
Kaepora Gaebora
Valoo
Ordona
Faron
Eldin
Lanayru
The Four Giants
The Giant Turtle
The Lokomo
The Great Fairies
Guardians of the Silent Realm
THE DEMI-GODS
Demigods exist in all pantheons. Demigods are usually the son or daughter of a god, or have obtained divine/spiritual powers in some other way.
For Zelda, those are
The Great Fairy Queen
The Ocean King
The Wind Fish/Levias
Cyclos and Zephlos
Golden Chief Cylos
Spirits of Good
SPIRITS
In numerous other pantheons, we have spirits, essentially anomalies in nature.
For Zelda, those are
Fairies
Season Spirits
Kokiri/Koroks/Kikwi
Skull Kids
Stalfos/Stalchildren
Poes
THE EVIL GODS
Every culture has evil gods. Surt, Satan, Deceiver, etc.
These are the evil gods of Zelda
Malladus
Bellum
Demise: Literally the Zelda equivalent of the god of pure evil. The Zelda devil, if you will.
Basically, it's a pantheon of multiple gods and goddesses.