Cubic crystals are real, common and well understood. Sodium chloride, ordinary table salt, grows in cubes because its sodium and chloride ions alternate on a cubic lattice, and the flat outer faces are that internal arrangement showing through at visible scale. Galena, fluorite and pyrite do the same. The insight that outward crystal form follows from a repeating internal structure is the foundation of crystallography, and it is a better story than any symbolic reading of the shape.
In scripture the cube appears as a deliberate figure for completeness. The inner sanctuary of Solomon's temple is described in the first book of Kings as twenty cubits in length, width and height, a cube, and the most restricted space in the building. The New Jerusalem at the end of Revelation is measured by an angel and found equal in length, breadth and height, a city in the form of a cube on a scale that is plainly symbolic rather than architectural. In both passages the equality of the three dimensions is what carries the meaning.
One frequent claim needs correcting. The Kaaba in Mecca is often called a perfect cube, and its Arabic name does carry the sense of a cube. It is not one. The structure is a rectangular block whose base measures roughly twelve metres by ten, with unequal sides and a height greater than either. Its significance in Islam has nothing to do with its proportions, and no Islamic source treats it as a Platonic solid.
Modern esoteric systems assign the cube to the root chakra, to the north, and to Saturn. These are twentieth-century developments out of New Age and crystal-healing writing, and they are neither classical nor Indian: the traditional element diagram for earth in Indian practice is a flat yellow square, and the classical chakra system uses two-dimensional yantras rather than solids. Modern sources also disagree about which solid belongs to which chakra, which is itself good evidence that the correspondence is recent rather than inherited.