wildkid
I found the solution (and it was very easy):
For Citra Standalone:
first set the language in Batocera ES under System Settings, Language
then while in Batocera ES main system selection press F1 on keyboard and navigate to Applications, and open Citra-emu-config, there go to system and set the language to the one you want. Then exit Citra and the File Explorer and start a 3DS game with Citra Standalone.
For Libretro Citra:
After you have done the steps above (setting the language in Citra standalone and start a game at least once to check if the language is then correct) just copy the folder share/saves/3ds/citra-emu/nand to share/saves/3ds/Citra and replace all existing files of the nand-folder there.