B&N had removed the links about a month ago. Last week they confirmed that the PC and Mac apps were no longer supported, and that they were now recommending that readers use the Nook for Web app.
It looks like B&N may have rethought abandoning support for the Nook for PC and Nook for Mac apps, though I'm not going to read too much into this. While the links may have been restored, the apps are still woefully out of date.
The apps were last updated well over a year ago. According to the website, the Mac app still lacks support for OSX Mountain Lion, which is running on 28 million Macs (around a third of all Macs in use). There's also no indication that the Mac app will be updated to support the recently announced OSX Mavericks, either.
I strongly doubt that either app will receive another update, so while the apps may be available to download they have effectively been discontinued.