Linus Elias Bo I don't think bunq "supports" your situation at the moment. Because you both signed up with a German address, your accounts default branch is the German bunq branch, which means Joint accounts will always have DE IBANs. Of course, there shouldn't be any issues using your DE IBANs while living in The Netherlands (I still use my old NL IBANs while living in Germany without any issues).
The real bigger issue you will probably face is not being able to use iDEAL and iDIN. Unfortunately, I don't think there's a nice solution here. I would definitely recommend bringing it up with bunq also through Private Support and ask them if they have any options for you after you both have moved to The Netherlands in terms of NL IBANs and/or iDEAL/iDIN support, but afaik there's no process to transfer users from the German branch back to the Dutch branch.