Actually, CS-Cart hooks are just the special places in the code where the developers are able to add any additional code with no influence or damaging some core platform codes.
CS-Cart structure has in mind hooks usage to modify, enhance or limit the functionality. As an example, you can change the cart functions using the PHP hooks. If you need to modify the template or implement a new CSS-style, you can use the SMARTY hooks. There are more details about hooking here.