There probably won't be a need to build very many ships. There are dozens of unique warship models for minor nations that were built for SH3 and SH4 - as soon as we figure out how to convert the models for SH5 there won't be very many ship classes needed. Nearly all of the important Japanese ships, for example, can be ported over from SH4.
It would be interesting if you could produce a "ripple effect" from the players' individual sinkings, as some people have already alluded to. If commodity stocks are modeled, it could create some interesting situations. Perhaps there could be several primary categories of goods:
POL (Petroleum/Oil/Lubricants)
Carried in: TANKERS
Affects: MILITARY OPS
CIVILIAN HAPPINESS (Gasoline, Heating Oil, &c.)
AMMUNITION
Carried in: FREIGHTERS
Affects: MILITARY OPS
FOOD
Carried in: FREIGHTERS, REEFER SHIPS
Affects: CIVILIAN HAPPINESS
MINERAL ORES
Carried in: BULK CARRIERS
Affects: INDUSTRIAL OUTPUT
TROOPS
Carried in: TROOP CARRIERS
Affects: MILITARY OPS
MILITARY STORES
Carried in: FREIGHTERS
Affects: MILITARY OPS
CONSUMER GOODS
Carried in: FREIGHTERS
Affects: CIVILIAN HAPPINESS
For instance, Player X goes out on patrol and sinks four British freighters and a British tanker in October 1939. Assuming all the ships were loaded. Britain loses, maybe, 2 points worth of consumer goods, one point of military stores, and one point of food, plus one point of petroleum products. The 20-30 U-Boats on patrol in 1939 will therefore sink an average of 5 ships per patrol, give or take a few. Over all, British resolve is shaken but not destroyed - after all, it's early in the war, and there are still a lot of merchants left.
A small number of U-Boats will be lost, based on historical averages for that time period. If the player's U-Boat is lost, then assume a higher U-Boat loss rate.
Democracies should be more sensitive to factors like civilian unhappiness, because they lack dictatorship's brutal efficiency. Also, countries like Britain and the USA should be accustomed to having more consumer goods than, say, Russia or Japan. If civilian unhappiness declines enough, then countries should suffer from civil wars, unrest, or even sue for peace. If petroleum/ammo stocks decline, it would be great if the campaign layers spawned fewer aircraft and naval sorties (shortages of ammo, aviation fuel, & bunker fuel).
Countries with smaller merchant fleets should suffer greater point penalties per merchant ship sunk. This can be mitigated somewhat if they have an ally with a large merchant fleet.
Sinking certain "prestige units" like Battleships should cause a large morale penalty/increase in unhappiness. The military would try to censor these losses, but of course word got around.
I don't know how much of this is possible - I'm just throwing out ideas.
