"Disproportionately, the datasets that are no longer accessible through the portal come from the Department of Energy, the National Oceanic and Atmospheric Administration, the Department of the Interior, NASA, and the Environmental Protection Agency. But determining what is actually gone and what has simply moved or is backed up elsewhere by the government is a manual task, and it's too early to say for sure what is gone and what may have been renamed or updated with a newer version.
This is because data.gov doesn’t always host the data that it is indexing. Sometimes the data is hosted directly on data.gov, but other times it links to an individual agency’s website, where the data is actually hosted. This means archiving and analyzing data.gov is not straightforward.
“Some of [the entries link to] actual data,” Cushman told 404 Media. “And some of them link to a landing page [where the data is hosted]. And the question is—when things are disappearing, is it the data it points to that is gone? Or is it just the index to it that’s gone?”"
https://www.404media.co/archivists-work-to-identify-and-save-the-thousands-of-datasets-disappearing-from-data-gov/