Since this phenomenon is something that Moffat and company have not continued, it's kind of a closed chapter in Who history. The sites are now winking offline as the BBC finds fewer reasons to maintain connections to that era of the program.
It's only going to be harder to justify the use of these sources on in-universe pages, since they can't easily be experienced by modern audiences. And it should be pointed out that they're not in great use now: only about 150 ns:0 pages use the link WEB.
I think we need to take a good, hard look at everything at wikipedia:Doctor Who tie-in websites — sorry for the wikipedia link but our list is pretty incomplete — and consider whether the right approach might not be to consolidate all known information onto real world pages and to phase them out of use on in-universe pages.
We could maintain and indeed improve our coverage of these sites by not having to work them into in-universe articles. Since many are not narrative, we could focus our energies on describing them on their own, real world pages to make sure we really got a sense of what the sites contained.
This approach, it seems to me, would be doubly useful because several of the sites have multiple iterations. Some of the citations which currently exist may well refer to a version of a site that no longer exists. By restricting their use to just archiving, we'd do our readers a better service than trying to figure out which are valid, narrative sources and which aren't. Plus, it's awfully difficult to discern between the two types since some of these sites have pages that are arguably narrative alongside pages that aren't.
I say we should declare all of them invalid — principally because their content is variable over time. That will then free us to systematically look at their archived history so as to create more complete picture of them for our readers.