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
Or perhaps they just leave.
it's not rocket science.
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.