The article seems to be suggesting that the Million Dollar Home Page has in some sense failed to fulfill it's promise because many of the links are now dead. I don't follow that logic at all. To me it seems that the MDHP's job was to be an iconic piece of internet history, and they've entirely fulfilled their end of the bargain.
The article uses the Million Dollar Home Page as an example of an interesting historical artifact that tells us a lot about the internet of 2005 in terms of design, the context in which the page was created, etc.
However, Million Dollar Home Page is also used as an example of the complexity of archiving internet content, i.e. archiving a page in a complete way must also involve archiving the pages it links to, otherwise the functionality of the archived page will decay over the years. This has important implications for its usefulness as a historical artifact.
Most of us remember what the internet was like when the Million Dollar Home Page was created, but many years from now, it will be challenging for people studying the history of the internet to really know what it was like back then unless we archive things in a way that preserves functionality.