If you have a WordPress site and we are able to connect to it, yes, your site will be automatically updated to the latest version when you open a malware removal request ticket.
If you have any other type of CMS, we will not automatically update your site. However, we will do whatever needs to be done to get your site cleaned and up and running. So we can update your site if necessary.
If your site is highly customized and cannot be updated, please do not open a malware removal request. Simply open a New Support Ticket with your FTP/SFTP information and say that your site cannot be updated. Your site will be cleared the same way but it will not be updated.