If you fast travel to places it will start you on the dock by your ship with your hood up. If you walk onto your ship his hood will come down and go into dynamic mode. But if you just run into the city his hood will stay on. You can also change outfits at a general store in town and his hood will remain up until you walk onto your ship. I hope this is intended because I love the assassin hood. I think it's cool he sails without the hood but when I'm on land I like the hood.