Having been in that space at the time, I think this point is not arguable at all. Freenet was not the first decentralized file sharing system. Freenet might have been the subject of a PhD thesis in 1999, but by the time it became even slightly usable Napster and Gnutella already had substantial user bases. (Similar to Ceph BTW which had a long gap between being a PhD thesis and being an actual usable distributed filesystem, during which time others had existed in the wild for some time.) The "arguable" part is whether you could include eDonkey, GNUnet, and others in that list. What is true AFAIK is that Freenet was the first such system with things like censorship resistance as a primary design goal (though the MojoNation folks might even disagree with that) and a non-trivial user base.

In case anyone doesn't believe me, here's the Freenet thesis which actually mentions both Gnutella and Napster in references. Hard to claim precedence when that's the case.

https://www.cs.cornell.edu/people/egs/615/freenet.pdf