As a DM, I'd apply the bonuses even if the ranger doesn't know he's dealing with his favored enemy - though I might not tell the player I'm doing it.
I can easily picture a ranger as having developed certain tricks and cues that he uses all the time, but against certain opponents (i.e., favored enemies) they're particularly effective (i.e., favored enemy bonus applied). In the example given, that guy may look human, and the ranger may think he's human - but he acts/fights like a shapechanger, and the ranger's methods are particularly effective against shapechangers.
Of course, I also view rogues as always aiming for the vital spot, but under certain circumstances (e.g., denied Dex bonus) that targeting is particularly effective (i.e., sneak attack damage applied).