It really depends (as much in cartography) on the focus of the map itself. If the map isn't overly concerned with the minutiae of political divisions in the Greek peninsula, it's not going to detail exactly where every city-state is, or the boundaries of their alliances. It's essentially the same thing you see with maps that show "Celtic tribes" or "Germanic tribes" covering the same general period of history- these areas also had many smaller factions within their "borders" (using that term loosely), but for general purposes the map is more concerned with showing cultural boundaries than the details of all the small, regional players within those cultural areas. It's worth noting that, particularly on a larger map of the Mediterranean, depending on the time period any individual city state isn't necessarily going to be hugely influential in the grand scope of Mediterranean politics.

Basically, the important thing to remember about maps is that any given one is only going to be concerned with the information its drawer saw fit to convey, which is rarely "everything."