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.
Or perhaps they just leave.
It's my opinion that hiding menu items not a great idea for the reasons OP said. In my opinion, coming from someone who's had to use an interface which does this, is that it's borderline obnoxious expecting me to remember where, and that it's necessary, to hover over magical areas to show important controls.
I think having the items be very translucent until hovered provides the best of both worlds. I can see where they are, but are easily ignorable.
it's not rocket science.