The sphere was probably styled to look like a green zamor, since thats what the piraka, the years first mainline sets, heavily featured. Im not sure where your getting the gemstone analogy.
Beyond thst, the holes and shadow were most likely just arbitrary graphic design choices, if you want to look further Id reccomend graphic design/art forums instead of a lego one.
In general with bionicle, despite its depth, Id remember it was primarily a toy line for kids and not read too much into it.