Why is GOG's version only in English, while physical versions have many other languages (French, German, Spanish, Italian and even Japanese)?
GOG should really add these languages in their preservation program

I provide translations archives to turn the English version into a French one, here: https://www.gog.com/forum/sid_meier_s_alpha_centauri_/fr_alpha_centauri_une_traduction_complte/post1

But I agree that all the localisations should be directly distributed by GOG, not provided by customers themselves.

Agreed. I have both Alpha Centauri and Alien Crossfire in the Spanish physical release, and both are fully translated (text and voice). And I must say, the dub work is fantastic.

So GOG, is there a copyright issue with the localized versions? or is a lack of availability of the files from the developer? Is there any way in which those languages can be added?

There's a Russian translation on zoneofgames .ru (can't post links for some reasons, sure you can find it if you just search for the name of the game)