i think there is not much logic behind this, its mostly a convention with weak logic and tradition.
if you are in sea or desert and you want to know the directions, obvious choice would be to get them by using a magnet. it can easily give you the north and south direction so either of them could be used as reference. north was chosen as reference point for direction because it might be used to calibrate the compass in night, using the position of Polaris star which was thought to be in north and static in sky. the polaris was used as reference in ancient time by sailors or travelers. in continuity to that established tradition, the north was established as reference even in modern time.