My college days were back in the '60's, so yellow highlighters and marginal notes might be passe. However, based on my experience with the Nook, I would definitely recommend the old-fashioned method.
The Nook is not 100% reliable. Scanning the subject lines in this forum confirms that problems do arise. I don't think the convenience of the Nook is worth the risk of losing all your notes.
If you ever had to do an "erase and deregister" procedure, it's a Nook lobotomy. ALL your highlights and notes would be deleted.
Good luck at school ...
For me this would have been an ideal solution, but then I was never a highlighter, and I always jotted my notes down on separate paper. My mom has wished that we had had this option (especially with the free classics from Gutenberg.org) back when we were kids, since it seems every kid in the family had the same books assigned in English classes, but never checked to see if we already had a copy. So we ended up with numerous copies of everything from King Lear to The Scarlet Letter to Trilby.
As far as the page numbers being inconsistent, it was common in such classes for different students to have different editions, so normally instructors would reference chapters, rather than pages in a particular printing.
As a lightweight way to carry many books, the NST is good., On how the NST does pagination versus how the Kindle does pagination verus how either compares to the pagination in a printed book, you'd need to look around.
My memory is that the Kindle does a better job of echoing the pagination from the paper books, at least by default, but there might be a setting that lets you get there on the Nook?
On highlighting and notes: ereaders don't do that at all reliably or well. The one exception here is on the tablet side, where you can get - as programs - editions of the Bible that are actually programs for displaying the text and maintaining a database in the background. And even there, I can't speak to how well it really works, but there have been people working on that in the context of the Bible pretty much since there have been personal computers. There is at least one dedicated, documented database system for tracking chapter and verse that notes and highlights can plug into.
I wish that some enterprising soul would look at adapting that for a wider variety of folks who read professionally, but I don't think anyone has yet.
I'd think that attorneys, academics and screenwriters would pay for an app that let them take an arbitrary epub file, have it parsed by a simple content management system (automatically, without their having to know what a CMS is) and be able to take notes and such with the notes being archived for them.
In theory, the Nook software does this, but in fact, there are tons of reports of folks losing highlighting and notes once those start to be complicated. I haven't looked at this myself, but suspect the problem is that the Nook system isn't actually unpacking the epub file and dumping the text into a database, but trying to keep the epub container intact and making use of lots of pointers, which all-too-frequently get hammered as the source file is reloaded for reading.