The habit boils down to essentially the treatment of applicants for jobs. Ages ago before the wonderful invention of email, some companies decided not to send out "acknowledgement of application" or "thanks but no thanks" letters as a cost saving measure. Since the invention of email and the ubiquitous use of online and email applications, there is absolutely no reason not to send these little notes out. Yet many business still do not and it simply is not a good idea.
The application process is a chance for business to build a network and good-will. A fanbase, if you will. It is also an opportunity to make some enemies. These days applicants share their application experience through Facebook, Twitter and other social media. If they have had a good experience, ie the online form worked smoothly, or an email was sent to acknowledge receipt of application, or a nice "thanks but no thanks" email was sent, then they will feel good about the company and most likely share those good vibes with others. On the other hand, if they feel that their application disappeared into the ether and they received no receipt or thanks for applying note, then they are going to share their disappointment or their anger.