In EU4 it's already hard enough to select some islands, eg Malta, especially when there's an army stationed there or a fleet in the harbor. In Project Caesar, there should be some sort of bubble on the map around small islands, to make it easier to click and select the location. Perhaps visible, perhaps not if the island itself is large enough to see, even when not large enough to click. If there are small inland locations, the first that comes to mind is Vatican, then a bubble may not be good. Perhaps a box with the location's name in a nearby large location, whether sea or land, and a line pointing to the actual place of the first location. To access the location, click on the box instead of it's actual place.
EDIT: grammar