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This article is actually about Onion Services on Tor, not "dark web" sites which are an entirely different thing. Onion Services are notoriously transient, so fluctuations like this are to be expected. You would need much more long term sampling to establish any kind of trend in the number of sites.
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By its very definition, the "dark web" is part of the "deep web" which is not indexed by search engines. This makes it inherently difficult to study. The original source of this article has some more details about the OnionScan tool that was used to discover this information.