In a lot of cases (and most of the Zelda series of games) a gimmicky 2nd Overworld is in order (Light World/Dark World, Seasons, Twilight Realm, etc.) Even the original LoZ had a 2nd Quest with similar but different OW. Each of these are essentially on-top of one another or mirror images/echoes of each other.
Phantom Hourglass and Spirit Tracks have whole different regions that might translate into 'other overworlds', as does Twilight Princess and Skyward Sword, depending on how big you make your regions.
But it really depends on the scope of your project. If you are building a grand saga spanning multiple continents with diverse ecosystems, you might have two or more OWs. But if you find yourself throwing in lots of 'filler' screens just to take up space, you might be able to get away with just one. One of the features of LoZ was the microcosm- a whole universe in one (seemingly) continuous OW.