To some extent, corporations helped mitigate the "extra resources are useless!" factor in Civ, because you trade the ones that aren't corporate for the ones that are...but they only appear in the last quarter of the game.
Scarcity could be factored in somehow (as in, not all cities in a very large civilization get the benefit of having a resource unless you have multiple sources), but that strikes me as complicated.
For strategic resources, I have suggested the idea that each source of horses or metal would let a single city train those types of units. Once you ran out, there was a production penalty (so you could have all your cities making axemen, but you would get a production penalty because you were running out of copper). No fancy stockpiles or anything like that, just a simple per-turn calculation.
