Not really, it would specifically depend on the actual production process that Intel uses. My best guess would be that the IHS is added at or towards the end of the process. Under those circumstances, I highly doubt that additional overhead generated from transferring the CPUs from Work in Process to Finished Goods at that stage of production would exceed the material and any labor costs associated with installing copper heatspreaders.
This is of course assuming that these "naked" CPUs would be a mass produced product line, and not made to order. Under the latter, the production costs could potentially go up. However, Intel already mass produces Ivy Bridge CPUs with no IHS -- the mobile line of CPUs. Those of course use a different socket, but with any well planned production process I highly doubt the costs would go up.