Hi MarkusL,
Thank you for that excellent question. That situation has crossed my mind from time to time. Before I begin, I would like to appologize for writting in English. Unfortunately I don't speak German. (I use Google Translate to read the German forums)
You can indeed create multiple stores in Bakery by simply creating multiple Bakery pages. Unfortunately there are many common settings which might prevent you from achieving your desired result.
Although I have not tried it, theoretically it should be possible to create several custom versions of bakery which each use different sets of database tables. I am by no means an expert when it comes to Bakery however I have a fair amount of experience customizing parts of it and see no reason why this should not work. You might also have to tweak it's integration with the site search engine if you want all of the different departemental shops to appear in the search results.
The bottom line is that the current version of Bakery does not directly include support for the features you are looking for about at this time. If the above workaround does not meet your needs, I would encourage you to add your suggestion to the following thread in order to be considered for future development:
http://www.websitebaker2.org/forum/index.php/topic,18426.msg128640.html#msg128640As for the groups, take a look at the list of upcoming features using the above link. I think there is something in the list regarding categories however I would be very interested in hearing your vision of how categories might be used.
Please feel free to contact me if I can be of service to you or if you are interested in contributing to the development of the Bakery module.
Have a great weekend!
With best regards,
Michael