I am pretty sure this issue has been up before. Try a search on this and the old forum and you might find some answers.
The skills do overlap a bit but to me navigation is the skill to find the way from point A to point B using the stars, the sun, a compass and/or a map as guide. Map reading is more about finding usefull information on a map. Information such as where is the best place to cross a river, which bridges will hold for a tank and where have the enemy most likely positioned their forward observers (maybe in combination with tactics).