So, in most polytheistic religions, the gods are not omnipotent, but scarily powerful. Generally, they are given domains over aspects of the mortal world, such as natural forces (Thor, Zeus, Posiden, Hades, Hel, Ra), or human concepts (such as gods of war, gods of love, gods of the home, ect) and typically have multiple domains that have a loose association (I.E. Hades has dominion over the Underworld, which grants him power over death, but also precious minerals, since you mine those from the ground. Posiden is the god of the sea, and horses... because he created horses... or he's the OG Brony).
With in their own domain, the gods of a pantheon are truly the end all be all power, but outside they are not powerful at all. Often, certain natural phenomena occur because the gods do not perform their daily chores (For example, Demeter is the goddess of plant growth, and is unable to do her job for six months out of the year, because her daughter Persephone must spend those six months with her Husband, Hades, and not her mother. This story was used to explain why winter is a thing and no crops grow.). Other gods such as Ra or Apollo are responsible for moving the sun across the sky daily.
An omnipotent god is generally going to show up in a Monotheistic religion (because it's kind of hard to be omnipotent if another being is equally omnipotent and can over rule your over rule of them). Generally, the reason for the seemingly absence of this type of god is that the deity isn't absent from the story, but he acts as a chess master of sorts. The heroes are there to save the day because the god decided that these heroes would solve this problem.
Other myths handle this by mixing Monotheism and Polytheism with the lack of interaction with the Big G God being explained as a limitation of the human condition to safely percieve this being, but all the little g lesser gods do not overwhelm humans and thus can interact with them. In many variants of Voodoo faiths, Bondye is the one true God and the Loa and Obeah are his servants and able to interact with mortals and represent their concerns to Bondye. In Hinduism, all divine beings are aspects of a supreme being who cannot be fully understood by humans and must present itself to them through a form they can understand. This is why Hinduism has an exceptionally large pantheon, even polytheistic religions, as there is no rule saying that a god from another religion (or in some cases a holy person who is explicitly not a god in the original faith) can be a god.
Most stories will either not address the issue, OR address the issue by saying that the gods have more important concerns (and by demonstrating that you don't want to become such a problem that the gods have to make you their concern) OR that the god has chosen to deal with the problem by maneuvering other mortals to deal with it.
In Christianity, for example, God granted humans free will, which allows humans to choose to not obey God. This is so important to God, that he would never interfere with free choice directly, but he may work within the bounds of his rules to influence others to confront the evil choices that have been made and stop them. From a narrative perspective, you will find that as the Bible progresses, God is less prone to smiting people for disobeying him as time goes on (Most of the wrathful God incidents are contained to Genesis and Exodus, the first two books of the Bible. In fact, Genesis stories could be summed up as "And then God said 'You did WHAT?!'").
