The 6" is diagonal; the vertical display height is 4.8". You haven't lost 2.0"; you've lost 0.8".
I have found some books to have margins that were set so firmly that they could not be adjusted below a certain level but it seemed to be a publisher option. Likewise some had font sizes I couldn't adjust easily. the only way I could really makes them readable was to reformat them through Calibre.
Still, it just seems annoying to waste so much space on the title and air. I know what I am reading, no need to tell me that...
There are two reasons I'm returning my nook and go back to my old Kindle:
1. As you mentioned, the header and footer. Why would someone need a constant reminder what book is being read? Does B&N think that we're idiots and thus need a constant reminder what we're reading? And why would the page number counter take like 10% of the screen? Other e readers like the Kindle take just a slim line for the page number and have no header. Anyways, if B&N cared about their readers they would release a software update that fixes this problem that includes a simple option to turn the footer and header off.
2. The home button. Every once in a while when I read I accidentally hit the home button. B&N should have made a haptic button which requires some pressure (like the kindle voyage) or just a simple manual button. Or - as a quick fix for the failed design - just include a tiny software feature to rotate the screen. If I set the screen upside down then the home button would be on top of the Nook and hence no danger to accidentally press it. Another fix would be to change the sensitivity of the button via software but I think that would be too much to ask.
Both of my reasons to return the Nook would be super simple to fix with a software update. Why wouldn't B&N invest a few hundred bucks to solve the issues?
For now I'm returning but should B&N decide to fix the two issues I'd be more than happy to buy one again. I switched from Amazon's Kindle to the Nook due to my love to B&N and because it's lighter than the Kindle as well as water- and dust-proof. Unfortunately the reading experience is still more important than some design features.