Frgive me for bringing up World in Flames again, but I believe its treatment of merchant shipping is both realistic and minimizes tedious micromanagement.
You assign convoy vessels to a sea area. For one convoy point, one resource can be transported through that sea zone. Thus, in order to transport e.g. 7 oil points from the Dutch East Indies to Japan, you will have to place 5 convoy points in every sea zone that has to be crossed (IIRC three in total). Deploying convoy escorts to these zones reduces the threat surface and submarine raiders pose to this line. If raiders should succeed in destroying two convoy points in the South China Sea, then only three oil resources will make it to Japan.
As you can provide air for convoys in coastal sea areas, you should be able to have the upper hand in naval logistical warfare, but in the Atlantic Gap, you face a more difficult task and if not deploying precious CVs there you are usually at a disadvantage. From 1943 onwards (or womething like that) the Allied Escorts become ever more efficient, accounting for decoding etc.
The Battle of the Atlantic (and elsewhere) can severely hurt the British war effort and also lend lease and resource shipping to a beleaguered USSR can be seriously hit (and obviously taking Murmansk, Archangel, Persia and Vladivostok completely isolates Russia, each conquest making resource transportation yet more difficult).
Escorting convoys also binds a significant part of the Navy, thus there being less available for offensive operations.
Personally, I am not quite convinced about the need to simulate a complex resource model. Oil and generic other resources should do the job. Food might be an interesting addition. Otherwise things might get too complicated and result in too much micromanagement, which might work in a turn-based game, but less so in a RT game. Manpower should also be another "resource".
Oil is used for plain consumption and transported to factories just as other resources. A possible food commodity would be nice chrome, but not vital. In an RT game things have to be kept moderately simple. The alternative is to have a economic and logistic AI which takes care of resource allocation, but I am skeptical about this being in the game, hence my reluctance.