Within our organisation wie would like to use NextCloud on the one hand as a data source (read only) for different groups, on the other hand each folder should contain a subfolder, where all group members could copy own documents to in order to share with the other group members. However, such a subfolder with different rights not only shows up at the users Explorer within the folder it belongs to, but also as a separate share in the NextCloud folder. Is there a way to prevent the folder with different rights showing up twice?
No, there is no nice way of doing that currently (as far as I know). You can use external storage and if this external storage supports that, it is possible (e.g. sftp/nfs to linux system and then with system permissions and for more complex cases acl). But you must manage the users and permissions on this external storage.