My understanding is that this is not really an error as it is an alert that a directive triggered is taking no action. Doesn't prevent the restart of the server in the end.
I can understand seeing the alert might still pose a nuisance, if that is the case then you should still have access to the httpd.conf files to remove the NameVirtualHost directive yourself. I've seen similar discussions in other forums like ServerFault that have indicated similar solutions to alleviate the message.
Could be just an error, but it doesn't look like it went through the motions of a restart. In the past when I restarted, it took a few seconds, and it actually gives you a message when the server stops and then another message when the server restarts, and the times each operation was completed. So you definitely know an operation took place. In this case, that NameVirtualHost error message occurs immediately and there are no other messages or indications that the server has been restarted.
When I tried editing http.conf through cPanel, I only saw the ability to edit a few things, you could not remove the NameVirtualHost code. I guess that would have to be done manually, but I'm only used to editing these types of files through the control panel. I did see the http.conf code via Putty but there are remarks throughout the file saying that whatever changes you make manually may get overrided by cPanel. Is there some sort of walkthrough guide out there instructing us how to edit that NameVirtualHost code correctly?