You can archive through the website. Just archive all the books you want to hide, then sync the nook. All the archived books should disappear from the NC (note that they will still be available to unarchive if you view archived books from the device).
AFAIK, you cannot sideload books to the iPad app (hopefully someone will come on and say that you can). If you can't sideload, then the only way to read an archved book will be to unarchive it.