When you set WordPress to multisite, in an “out of box” fashion, you create a single network of sites. Let’s, say, a network of food blogs.
With plugins like WP Multi Network you can set up multiple networks. You could split that food blogs network into several networks: mediterranean food blogs, brazilian food blogs, thai food blogs, wine blogs, etc
From what i grasp reading https://make.wordpress.org/core/2016/07/08/multisite-focused-changes-in-4-6/ and both classes sources (and their related functions/other classes), WP_Site_Query queries about existing sites in a single network (e.g. find all active sites in that network) and WP_Network_Query do the same across several networks (e.g. find all archive blogs on all those networks).
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