Unfortunately, CafeCommerce does not have the ability to specify the target for links that you add to the navigation. The suggestion has been posted to the the Feature Suggestion forum here: 1912673-target-attribute-for-external-links-in-navigati and we will update the status there if this changes.
The only option that would prevent this now is to not use External links for the pages that you place in the navigation. Then, you can add your own links within the content of those pages that you could specify the target attribute for.
We are adding a lot of features to CafeCommerce at a pretty fast pace and we will consider adding this functionality to the schedule as soon as possible.