Civ III had a similar system of strategic resources, IIRC it worked quite well since it meant that building an empire was more complicated than simply acquiring more cities than the competition; if you found yourself in a modern age war with no oil, you were essentially finished even if you had the bigger empire. It also meant the diplomacy system actually became useful, since if you had no access to a resource, you would have to trade for it with another faction who had spare, and then hope they wouldn't cut you off at a crucial moment. You could also wage diplomatic warfare, by pursuading your enemy's only supplier of oil to sign a trade embargo against them.

So yes, I think this could be a fun thing to add to Empires, since it makes the trade and diplomacy aspects of the game much more important, both of these being features which were rather underpowered in previous titles.