The style of the illustration should be in line with the style of other covers for nature publishing journals.
Thus, it should be modern and present a limited number of elements to emphasize the main subject of the article.
A 3D illustration is great to add a certain modernity.
3D is often used for covers because each subject is presented with a different approach than how we usually see it (different from what we can observe with a microscope for example).
But it also allows to have freedom for composition while also keeping a realistic feeling.
These two aspects are very important to create an "eye-catching" image on scientific subjects.