I think most of the symbols are meant to represent a culture (these are the symbols shown in the rebel units that spawn when you have low stability, for example the one you are hovering over in the screenshot would be the symbol for the "rebels from the Myceneans"). I believe most of them are based on actual empire symbols or, if we don't have information on which ones these were, they are based on motives that are frequent in a culture's art. For example this symbol is an octopus motif that is found in a lot of Mycenean inscriptions, or the Carthaginian one is the symbol for Tanit, their main goddess. I think most of the symbols will follow a similar reasoning. You can know which symbol belongs to which culture because starting with the Assyrian double headed eagle they are all arranged by era and alphabetical order (there are some exceptions liek the Greeks, which are in the A position, I assume for Athenians; or like the Teutons, which were previosuly named Holy Roman Empire and are placed in the H, not the T, but these exceptions are easy to catch).