If you go, for example, to Ukrainian wikis, and click on one of the links under "In other projects", namely Wikimedia Commons, Mediawiki, Meta-wiki or Wikispecies, you'll always get to the English versions of main pages there, while all these sites have localized ones for Ukrainian.
In this message on translatewiki it is stated that the links are chosen based on Wikidata data. The problem is that the appropriate Wikidata item doesn't allow localized names of the sites mentioned above. I tried to add a separate item for "said to be the same as", just like it had been done for German and Czech, but it didn't work. It doesn't work for German and Czech either.
I can see that only Russians managed to fix that, but I cannot figure out how they did that (perhaps it's been hardcoded somewhere?).
So my suggestion is either to enable the translation of the appropriate messages on translatewiki, or provide some Wikidata means to add the appropriate links.