Naval Architecture: while marine engineering deals mainly with the maintenance of marine machinery, that is to say with the operational aspects of a ship, naval architecture deals with the design and construction phase of the vessels. Just as an architect creates a blueprint for a building or a structure before it is actually constructed, similarly a naval architect creates the plans, designs etc before the actual construction of a vessel commences.
Nautical Science: a vehicle is not much useful without the person/s used to run or operate it, and this is true for all types of vehicles including automobiles, manned spaceships and so forth. Of course the difference lies between the level of sophistication of the vehicles and the technology used. For example a car is a pretty simple technological device (relatively speaking) as compared to a spacecraft which requires specialized training and knowledge to operate it. Marine vehicles fall somewhere midway and require personnel with specialized knowledge of nautical science to operate the vessels.