I got the 3-in-1 version. I found it very easy to navigate, and you can't beat it as a good buy.
I haven't tried the 3-in-1 edition, but I have purchased the three individual eBooks from B&N. Interesting tidbit: It is believed that Tolkien original wrote LOTR as a two volume set...the publishers decided to make it a trilogy.
The footnote links work well, but I had to place a bookmark on the page I was on before I followed the footnote link so that I could get back to the original page after I was done reading the footnote. Perhaps this was user error -- but worked ok as a process for me.
The maps are very difficult to see on the Nook (in my opinion). However, the maps looked great when I was looking at the eBook on "Nook for PC."
The story I heard was that Lord of the Rings was a single novel.
When the publisher balked at releasing something that size Tolkien simple divided the book into thirds with no modification to make them stand alone books.
Which is why there is no real conclusion to the first two book, You must read the entire trilogy.