Based on the discussion in this thread, a system is now decided on. Geoff has written up these results into the wiki, which I've duplicated here. Thanks for your help, and look out for the next design thread soon.
A ship hull has various "slots" in it that may have one or more ship parts placed in them.
Slots are characterized by:
* Size - Slots may be one of several sizes, such as "small", "medium", "large", etc. Ship parts have a size, and may only be placed in slots of equal or greater size. Multiple smaller parts may be placed in larger slots (specifics to be determined).
* Internal / External - Some parts (including some specific weapons or engines) may only be placed in external slots. Other parts may only be placed in internal slots. Other parts can be placed anywhere. External slots are more prone to being damaged by weapons fire hitting the ship.
* Facing - External slots are located on a particular side, or facing, of a ship. The facing of an external slot may affect the function of parts placed in it, such as by limiting the directions in which a weapon can fire. Facing may also affect the liklihood of a part being damaged by weapons hitting the ship from the facing direction.
There may be various differently-shaped hulls of the same size. Different shapes of hull will have different numbers, sizes and configurations of slots, while having overall about the same total space for parts. One shape might have fewer larger slots, and another might have more smaller slots. Alternatively, there might be more forward facing large slots on one shape, and more internal and side-facing large slots on another shape.
Shapes might also have characteristics that directly affect ship performance, similar to sizes, or may not.