why include an instance that doesn’t?
Because it lets you see how common or uncommon defederations are relative to the total set of all instances (or at least, all minus the long tail of very-low-user-count ones). And although it would make the graph larger, it would also make it sparse and IMO that would also be easier to read.
It could also give a misleading impression that all instances defederate or are defederated by somebody, making people think it's more common than it actually is. (Or maybe not doing that, if you include all^ish^ instances and it still ends up being not very sparse.)