In the Azumanga Daioh English localization, the English is...in English, but in a different font and with a footnote. The reason Kaoru learned German in the first place is because of the time she spent with a German foreign exchange student. Changing that part of the story and having her speak in an entirely different language when they could just put the German in a different font and/or include a note seems pretty unnecessary, but it's ultimately up to the publishers. I think it would be pretty cool for German readers if they knew she was speaking their language.
It seems I recall incorrectly. I found one page where Osaka speaks Spanish, but that's because a foreigner spoke to her... in German. Must have been some other manga with a school setting. I'll get back to you when I've re-read everything on my bookshelf; it shouldn't take more than twenty years at the outside.
I also failed to recall that Kaoru had a specific reason to know German, as opposed to (say) Swahili... Yes, probably best not to change that, in case it becomes an important plot point later on. You never know.