The disadvantage of this is that there is no visual cue to the user that additional controls will appear. Not every user will spend time hovering over your entire UI, searching for controls that you've hidden away. This is a one-dimensional design decision. "UI looks cluttered, lets hide some stuff. Wow that looks better!". But from the viewpoint of a new user, you've just created a barrier.
Have you conducted any studies that show that? We have done this and so far no one has ever complained about "missing links/buttons". Most users never even noticed when we switched to hover controls
it's not rocket science.