The abundance of elements on Earth comes from the abundance of elements in our part of the galaxy. And the cause of that is that the galaxy started entirely hydrogen and oxygen, with the heavier elements being manufactured in stars. So the concentrations tend to get higher as the atomic number gets lower.
For the second question, it depends what you mean. Nitrogen in the atmosphere is a diatomic molecule. Many elements are free and dissolved in our oceans. Crystals (monoatomic) are essentially locked-together piles of atoms. You probably should call them molecules, but then even an atom sitting all alone is generallly also considered a molecule.