One thing that I found rather annoying is that if you are not defining Remote or Testing information BUT the check box is still checked for that configuration, then you will still get the _notes folder created.

For instance, I do not define Remote Info on my sites. So, I had to go into each of my Sites, Goto the Remote Info Section (in Advanced mode), select Access to anything other than None, uncheck Maintain synchronization information as well as Automatically upload files to server on save – to be certain – and then set the Access back to None.

Once I did that on all my sites, I _notes folder was no longer magically appearing.

Hope that helps you situation.