People have been using tables of contents and indices for books and other printed materials for a long time, but those are redundant in the era of CTRL-F. At best, they're useful only as an adjunct to searching digital content.
Likewise, imposing archaic methods of organisation on modern storage is sub-optimal. The argument is to move toward something that makes more sense given the capabilities of the medium.
What tags and searching do not provide is context. One affordance that putting files into a folder provides is reminding oneself that when I look at file A, I should probably remember about file B too. Later I may even forget about the existence of B, but when I go searching for A I'm going to see B as well.
Search and tagging are not contradictory to cataloguing. They're complementary.
It's also not true that old media didn't have any search facilities. Old technical books would each have an index of keywords at the end. That's search, just analog and requiring a bit more work from the publisher. This index didn't make the table of contents redundant.
Likewise, imposing archaic methods of organisation on modern storage is sub-optimal. The argument is to move toward something that makes more sense given the capabilities of the medium.