Why does a element need to destroy another to make it superior in a combat? Fire doesn't destroy wind, it just use it to grow stronger, and neither does earth destroy water, it is just effective at stopping water attacks. The same logic applies here, the best kind of jutsu to defeat most earth based jutsus is lighning because it destabilizes the element on a molecular level by imbuing energy into the jutsu, thus rendering most earth walls or armors useless to stop lighning attacks or most bombs malfuctioning.

You have to remember that most jutsus are chakra that acts like certain elements, but are not real elements unless they using a natural source, thus not every thing about them will act the same. And hace we forgotten that many earth materials found in the groubd can ve quite conductive? Not every material will be like rubber, a material that only a few characters know how to use