Hi,
1. Deleting the images on the drive won't help as the issue is that you have the image entries in the hikashop_file table of your database for the images.
You will need to run such query via your phpmyadmin to clean that table:
DELETE n1 FROM #__hikashop_file n1, #__hikashop_file n2 WHERE n1.file_id > n2.file_id AND n1.file_ref_id = n2.file_ref_id AND n1.file_type='product'
Please backup your database before that operation....just in case. And make sure that you replace #__ with your table prefix.
2. Having the add to cart showing on some products listings and not others is normal. When you edit your products listings menus/modules via the menu Display->Content menus/modules, you have an option there to display or not add to cart buttons for that particular listing, overriding the default setting of the HikaShop configuration.
If you don't want the add to cart button on your listings, then you should edit all your products listing menus/modules and make sure that this option is turned off.