That was probably when we switched the web site repo from having independent copies of the meta-schemas to using submodule references to the specification repository. So it wasn't intended to be a change. AFAIK that "links" section was always supposed to be there. and if it was missing that was a bug. It just makes the hyper-schema meta-schema a hyper-schema on its own, which can identify it's own URI. Which is nice more for philosophical consistency than anything else.
Other than being unexpected, does it cause problems? If not, then you can safely move on.
Our expectation is to only ever update those meta-schemas with actual bug fixes. The change you saw has to do with weird decisions to duplicate the files in the past, which let them get out of sync with the spec.
thanks,
-henry