In my own homebrew setting I've kept it rather simple, so my players can at least remember most of the deities.
I have three ancient evils, which are god-like in nature, and only worshiped by the villains.
I have one pantheon of good/neutral gods, 5 of which are referenced repeatedly in the campaign. Priests in my setting worship all of the gods in the pantheon, but only 5 of them are always prominently on display in every church. The other gods may have a small shrine/statue in a corner of the church; always represented, but depending on the church, other gods may get preferential treatment. For example, the goddess of love and fertility is only worshiped when people want to have a child, have marriage problems, or when a big festival is approaching. So, this goddess is not prominently on display, and the players have little interaction with the deity.
Lastly, some churches have a local saint, which the church tends to be named after. So you might have a St. Anna's Church, or a St. Germaine's church. These saints are only worshiped locally, but pretty irrelevant anywhere else in the world. I use them mostly to justify the name of a church, and to give a little backstory to its founding.
This raises the question, why have so many gods at all? For my campaign, I find it helps with immersion when an npc mentions a deity in casual dialogue. It makes the world feel more alive. But its not important to me that my players know the names of all the gods by heart. I'm surprised by how many they remember by name though. They know the goddess of the sun, the god of death, the god of storms, the lesser-goddess of sailors, the god of the moon, the god of trickery and the god of protection. That's a lot of names.