Deploy fleet sends your fleet to a certain town. Any blockades can not see you coming, because your mission is not hostile. As soon as you get to the port and there are enemy ships there, you will engage in battle. Defend port alerts the enemy ships that you are coming to defend the port, since the mission is hostile. I am 22 hours away from my alliance, so I use deploy fleet when sending ships to help a member so that the enemy can't see me coming. He only sees once I get there, and start attacking his ships =)