How can I delete unused categories or categories with no products in them?
On the Products -> Categories page expand the whole tree. You will see the amount of products in the category in the Products column. Select corresponding categories and use the Delete selected option to delete them
Some of the categories have sub categories. This would delete everything inside them.
Yes, you need to be careful because root categories my show 0 products but still have subcategories that do. You just need to keep expanding the category until you get to the bottom then delete those categories that have 0 products.
I have over 600 categories that seems to have been inserted by an import into the wrong locations. I may just have to remove them all and start again. I think cs-cart still need a lot of work! I did post ideas however them seem to decline most of them.
Some of the categories have sub categories. This would delete everything inside them.
Yes, but the tree look and feel is quite clear. You can see, if the current category has subcategories.
If it is not suitable for you, you can create special script which will make requests to database and delete required categories.