I do not agree that Automatic submission hurts the site or lead to some sort of BAN on the site.
However Automatic submission will not work in good directories because of the following reasons. So it is pointless to do the Automated submission. When I started my career as SEO I bought Dynamic Web Submission for $500 which claims to automatically post to 1000's of directories. I had used it and tested about 5 sites but not able to get a single good inclusion.
I then did a lot of trial and error experiments with IBP etc. But nothing works.
These are the reasons why an Automated submitter will never work.
CAPTCHA (IMAGE Identification) Almost all the directories will ask you to identify the characters in the randomly generated image while you do the submissions. This is possible only in manual submission.
Different categories Some directories have as less as 25 categories while others have more 3000 + categories. The category names are not consistent across the directories. Manual submission is needed to submit the web site in the right category.
Different types of form input. Some directories will ask for very few details while others may require much more details like having an user account to do the submissions. Providing appropriate data according to the directories is possible only by manual submissions.
Confirmation Most of the directories need a confirmation by which you have to manually click a verification link sent to the email and confirm that the submissions are done manually.
No automated software or service can take into account the above features of directories while submitting the web sites. The fact is most of the directories do a manual review on the submissions and will find out the automated submissions sooner or later and block them.