Deeply nested code can be challenging to read and understand, as each level of indentation adds complexity and additional conditions for the reader to process. To enhance readability and maintainability, one can refactor code by reducing nesting through methods like "early returns," which involve inverting conditions and returning early. This approach simplifies code, making it easier to read, modify, and maintain. The advice encourages keeping code flat and simple, benefiting both current and future developers working on it. Practicing refactoring techniques can further improve one's coding skills.