Lots of religions have gods at varying levels. Hinduism for example, as well as the Ancient Greek and Roman religions.
My personal take on the Zelda pantheon is something along these lines:
So you have the 'actual' goddesses, which are Din, Farore and Nayru. They created the world and everything in it and left the Triforce behind. Then you have Hylia, who is like the 'goddess' of the people, kind of how Jesus was like God on earth or whatever. Perhaps it is possible that she had godly powers just to protect the Triforce and everything in Hyrule. Kind of like there was all this power, and the Three Goddesses are the origins of it, but Hylia was the one who wielded said power.
Then you have the deities which, like the Sikh Gurus and Islamic Prophets, are dotted across time, from the dragons in SS to Lord Jabu-Jabu and the Great Deku Tree in OoT to the Light Spirits in TP (I'm not going to go into the debate as to whether they're the same essential beings reincarnated at this point, I'm going to treat each era of Zelda as it's own for sake of explanation). I also think that the dragons/deities are some kind of 'earth' versions of the Goddesses, given the similarities in names. (Eldin, Lanayru, Faron)/. This would reinforce the similarities in a way with the Ancient Greek beliefs in the sense that their Gods were also able to interact with the world.
I believe the Sages only came to exist after the Triforce was first sealed into the Sacred Realm, and they were then in charge of protecting the Triforce. I think that when Hylia was reincarnated as a mortal, was p much defeated if it wasn't for the Chosen Hero and so forth, the powers that be decided that a single guardian for the Triforce was too weak to properly protect the Triforce, so the task was distributed to the Sages once the Triforce was sealed away into the Sacred Realm for protection. It's much harder to defeat 5 people with almost godly powers than it is 1 because they won't all be in one place. Obviously though, this fell apart when the Triforce split and Ganondorf was able to subdue the Sages with the Triforce of Power. It's obvious in some senses though that the guardianship of the sacred realm was kind of the point of the temples in OoT, at least.
Then you have the fact that separate deities/religions seem to exist further down the line amongst different groups. It's obvious to me that the Gerudo believed in the Three Goddesses religion but they seem to have their own deity just like the Zoras and Kokiri; however, the main difference is you know basically nothing about the Sand Goddess or whatever you want to call the woman the OoT Spirit Temple features (similarly depicted in the Ancient Cistern). It would make sense that there are almost different denominations, especially when the culture is clearly different as is the case with the Gerudos, but Ganondorf was evidently aware of the Triforce, and not just because he is Demise's reincarnation, but because Twinrova made him aware of it, which means that there was at least general knowledge of the Hylian religion. If being King of the Gerudo is in any way the same as being the King of England back in the day, the people generally follow whichever religion their ruler follows/imposes unless there is enforced secularism- and somehow I dount that Ganondorf is the most tolerant guy. I also happen to believe the Sheikah also clearly believe a slightly different version than the general Hylian population, but that the basic principles of it are there in the fact they guard the Royal Family, the descendents of Hylia via SS Zelda. Maybe the Sheikah are sort of like a 'chosen people' which predate SS, given the fact the first Impa already exists in that game on the surface.
So, to summarise:
Actual Gods: Din, Nayru, Farore. (Creators of the Triforce)
Wielder of godly powers/protector of the world: Hylia (Protects the Triforce on behalf of Gods), Sages (protects the living world/sacred realm from Demise)
Earthly Gods/Deities of Worship: Various
Denominations: Various (see different deities, cultural differences, variations in beliefs between people and between games)
Chosen People/Peoples of Note: Sheikah, Gerudos (possibly)
P.s. I did not discuss the Four Giants or any other part of MM as I feel that Termina is a whole different ball game from Hyrule.