All of the questions asked are very broad in their scope. I will do my best to answer each on some level...
1. Almost everything needs to be taken into account when designing a new harbor! Global Scale - defining the purpose of the facility...is it for local fisherman, for a specific maritime purpose, or a global trade center. Local - define the existing site characteristics - soil good for foundation, is the site permittable, is skilled labor available nearby. Coastal and Marine - What are the water depths near the site - can the ships of the harbor pass safely under all tidal, storm and wave conditions? Is the site protected from the dominant waves...from small waves?
2. Squat is the downward displacement of a vessel while it travels in shallow water. If you look at the Bernouli equation - if no energy loss is assumed, then the total energy must stay the same throughout the fluid. Under a ship with low clearance, the water must move faster under the ship than at the sides or adjacent to it. As the velocty increases the hydrostatic pressure decreases effectivey sucking the vessels down. It is not very pronounced at slow speeds. There is a formula for it (I think). I'll post that later.
3. The requirements of a good harbor are difficult to define. There are so many! Reply to this post with more specific questions. A few are: Little wave distrubance, well maintainted structures, capable land based cranes and offloading equipment.
4. Littoral drift is the transport of sand and sediments due to the action of waves on beaches...in the general alongshore direction. Onshore-Offshore movement is called the cross-shore direction and typically associated with erosion/deposition from storms and incident wave energy. Littoral drift can clog the entrance channels and cause unnvaigable waters as well as dangerous wave conditions.
There aren't many good websites for all this but there are plenty of good books:
Kollmeyer and Tobiasson - Marinas and Small Craft Harbors
Gaythwate - Design of Marine Facilities for the Ebrthing and Mooring of Ships
Tsinker, Gregory - He has a couple and I can't rememeber the names. Look under floating ports or marine structures.
Look these books up on Amazon for better info.
Any questions, e-mail me at stevef@ocean-coastal.com
Steve