You will not find an option to delete categories in Store Commander's interface, it would be rather dangerous to delete a category from the database because you might also delete products included in that category.
If you need to delete a category, simply drag/drop it into the SC Recycling Bin.
Make sure there are no products in this category, and if there are, remove them by dissociating the products off that category, using the Category panel located in the Properties column - check the article below if you need more detailed information.
You can then empty the Recycling Bin by hitting the icon on the Categories toolbar.
Finally, do not forget to apply the option under Catalog > Tools > Check and fix categories - always recommended when working with categories.