Yes, Automatic Directory Submission is really a waste of time. And it won't affect your ranking, if you've submitted to many directories in a short period of time. Also, although you've submitted your website to many directories, your website would not be listed in the directory site until it is a paid submission. Usually, directories would take a minimum of a weeks time to list a website in their directories. So, submitting a website to too many directories would not affect the ranking or SERP.