I would say there is a very slight difference in meaning. As was already mentioned mood is usually mentioned as a positive or negative emotion. He was in a terrible mood after work. She was in a good mood all day long. But morale is a word that describes someone’s overall sense of well-being. Your morale would be low if you were down in the dumps (depressed). A team’s morale could be low if they were losing a game. An employee’s morale could be optimistic if he thought he might get a raise.