Yes it does. Hopped extract already has some IBUs in it so to speak. Unhopped extract has 0.0 IBUs in it. So if you had the same recipe extract poundage, hops, and yeast the only difference was hopped and unhopped extract, the hopped extract brew would be more bitter (higher IBUs).
I never have used hopped extract, but I'm sure you can find information on approximately how many IBUs are in it, at least you should be able to, if not the people making the stuff aren't using their heads.
As far as calculating IBUs, the formula would be the same regardless of which you use, only the hopped extract you have to add the IBUs already present to any IBUs from the hops you add.