I have been setting the .name property Prefabs I create during runtime:
Seeker a = (Seeker) Instantiate(myPrefab, new Vector3(20,0,20),Quaternion.identity);
a.name = "Red George";
I do this to make reading the Hierarchy outliner easier but it's not really needed for my project otherwise. Am I breaking the clone's relationship to the prefab? Are there other side effects like increased memory usage or mesh duplication?