Most people don't need to go into their Library folder. If you do, I suggest you're not typical. And Lion will in no way restrict your access to it. It's just hidden. This is going to be a good thing for most people.
You're thinking too small. Who says you'll only have one disk connected to your port? The bandwidth of Thunderbolt is supposed to be larger than that required by your devices so that you can put multiple devices of multiple types onto that one port.
I've got something similar going on here. When the video plays, I hear it but there is no video window. If I select full screen, the video plays normally but when I leave full screen mode, the video window remains gone. It's weird and I have not figure it out yet.