Hello Mat,
I don't think I'm seeing the same SERPs as you. Is there any way you could give me an example of one of these subdomains?
And yes, you're absolutely right that the same problem of keyword cannibalization would apply to subdirectories as well.
If it's the woltersk....lu domain I am getting non-secure warnings from Firefox when I try to access it.
How many different subdomains are there / will there be? Is it just shop.domain.lu and www.domain.lu or are there others? I didn't see any for "courses." or "software." in the SERP example you provided with the link. If it's just one, I think that's manageable. For example, maybe www. could focus on informational queries (e.g. JavaScript course) and shop. could focus on transactional ones (e.g. Buy Acme JavaScript course). Maybe one could focus on reviews and comparisons, or long-tail queries while the other focuses on short-tail queries. Without knowing more about the domains and your business, it is difficult for me to say. If you have three or four subdomains all going after the same keywords, that's definitely a problem and I don't think you can avoid cannibalization. At that point, it would be best to choose the strongest domain/subdomain and focus your efforts on ranking one of them instead of watering down your efforts over several.