Smart Slider 2 build up the Js and the CSS files into one file to speed up the serving of these resources. This behavior used on the admin interface too. This is why you might see multiple files.
So the answer for your question is yes, you can empty those folders(Also you can clear this cache in your WordPress admin/settings/Nextend settings/Clear cache button). The Smart Slider will regenerate the necessary files again when it shows.
Note: There is an exception for this process. When you are using full page caching with some other plugins, you might need to clear that cache too. If you just empty our cache folder and you have full page cache, when the page loads, it served from the full page cache and Smart Slider not initialized, so cache is not regenerated.