You dont have to go completely overboard with accuracy to please the majority of the customer base, we're no ESA. Warm water/air rises, cold air/water sinks. Divide into small enough zones - enough to create the impression of "real" wind/water currents but still computeable. Then you just have to make ships interact with the current.
X-Plane by Austin Meyers is using simplified dynamics for this since 1994 without stressing the computer. The basis of that game is to simulate, in realtime, the airflow around several cross-sections of any given foil (blade element theory). It is not absolute in accuracy, but close enough for several real aircraft manufacturers to use it for the developement of their aircraft.
Forza 3 is able to calculate friction and mass for 8 cars/32 tires 360 times every second (only slightly slowing the game down at even the most demanding of times) making a reasonably realistic impression of a car hurling down the track. I am not able to recall how many datapoints it takes into the calculation, but I know temperature and air pressure of every tire, several parts of each shock absorber and recoil spring, aerodynamics (scripted afaik?) and similar things.
You could also just do it the MS Flight Simulator way and script it. Far less accurate but it yields results faster at far less resource cost. Perhaps not that terrible a solution as there are no player made ships in SS, and it might turn out more practical to script the dynamic behaviour of each ship in relation to a given wind/water current strength than building an entire physics engine.
