In answer to your questions:
1) Users cannot list in multiple categories from the front-end, but admin can do this from the
wp-admin dashboard.
2) ClassiPress has the option to feature a listing to appear in the homepage slider, but not other additional featured ads options a you have described. On a related note, there are child themes available in the
AppThemes marketplace which add other options to featured ads such as highlighting or a ribbon
3) You can create different ad packages which allow listings at different prices for different durations, and although featured ad duration can be a separate charge, the duration matches that of the ad package its purchased with.
4) There is no separate pricing option for this built into the theme.
To clarify, ClassiPress is not encrypted, so you are free to make modifications to it as you wish. AppThemes does not offer customization services, however we do have a
certified partners page where you can find developers for hire. If you make contact directly with an outline of your requirements, they can provide a quote for the work. Thanks.