That's a somewhat naive viewpoint; the only mods that don't use Ubisoft's original content are usually graphics mods and other minor detail. Any gameplay mod, which are by the way in the majority for both SHIII and IV, involve modification of and redistribution of Ubi's data.
And if we want to really dig deep, Ubi did not ask permission to use some of my work for SHIV (which I don't mind, but that's a fact).
That said, I totally don't mind. And I totally agree that modders, as 'grey' as their area may be are beneficial to both the community and to Ubisoft.
But you need to be careful what you define as copyright. I again refer you to Professor Lessig. He does an excellent job of showing how the definition of intellectual property in the current law is flawed, and what's worse, fatally flawed in a way that kills creativity and may one day give us a permission-based culture where things like modding are simply impossible.
You can even read his book for free online:
http://www.free-culture.cc/freecontent/