1 - I build harbours and boats in every game and find them very useful for exploring, colonizing, and even carrying stacks from time to time, depending on circumstances. A good tactic is to transport a pioneer and a defending stack (along with a sovereign's kid - for the erosion spell) to a far away area where an enemy faction is located. Once the settlement is established, your sovereign can teleport a killer stack there and capture the closest city, which is usually not well defended. The key here is learning to use the level 3 spell 'erosion'. After casting the erosion spell, set your buidings up toward the water so that there is one complete beach tile between the city and and the water. It's ok if there is a small amount of beach around the complete beach tile. It is pretty tricky until you get the hang of it. Just keep experimenting! They can be built and they are especially useful if you download the Fish Market mod by Takoa21. Fish markets can double food production fairly early on in the game (when your city reaches level 3}. They will give you a nice edge at any difficulty level.
2 - Boats, once built, cannot be deleted - probably a bug in that regard. However, if you have no more use for them, they can be put to good use as early warning radar since they can act as watch towers warning you of approaching enemies.
3 - For either weapon or shield, you need 3 midnight stones. Note that the hut that gives you the quest is not the same hut that will redeem the stones. If you hover over the map with the cursor, the correct hut will be titled 'the blacksmith's forge'. Bring it there to redeem the stones.