The tags work really well for that, actually. Here's how I do it:
1. Before I add new books, I select all my existing books (control-A) and use bulk edit to add a tag named PROCESSED. calibre takes maybe 20 seconds to go through my thousands of books and tag them all.
2. I add my new books as usual.
3. I go to tag view and click twice on the PROCESSED tag so it only shows those books that do not have that tag -- i.e., my just-added books.
4. I do any needed editing, conversion, etc. As I finish each book, I give it a PROCESSED tag (generally at the same time as I'm adding whatever other tags the book needs).
5. If there are more batches of new books to add, repeat steps 2-4.
6. Finally, when I'm done adding books, control-A to select all books once again, and bulk edit to remove the PROCESSED tag.
By tagging the books you don't need to work on before you start work, "finding the books after the fact" becomes easy.
Remember that calibre is the creation of a guy named Kovid, not a development team of hundreds at Microsoft. Kovid is a genius, and there are other people contributing to the project, but it's still a volunteer effort being done by a small number of people. There are a lot of things people want calibre to be able to do, and a very limited amount of manpower available to do them. When there is a practical way to do something with the existing features, building another way to do that thing has to take a lower priority than adding the new features that people like me are clamoring for. The "purity of purpose" of metadata is less important, under these circumstances, than the requested features that calibre doesn't have at all.
Try my way of doing it; you'll find that it works very well, and after you've used it for a while (I have processed over 2,000 books with that system) you might find that you don't need another mechanism after all.
Incidentally, I don't know much about the Nook, but if it has both primary and secondary memory, like my Sony Reader (internal and SD card), another good use for tags is to differentiate which books go to which area of memory.