I got the sames problem when I created an XmlElement like here
XmlElement xmlElement = myXmlDocument.CreateElement("MyElemenent");
myXmlDocument.AppendChild(xmlElement);
after this I got the attribute xmlns="" after saving.
If I use the namespace of the document I could suppress this xmlns attribute.
XmlElement xmlElement = myXmlDocument.CreateElement("MyElemenent",myXmlDocument.DocumentElement.NamespaceURI);
myXmlDocument.AppendChild(xmlElement);
Without the empty xmlns="" my SelectNodes didn't work anymore because the namespace needs to be specified. Solution for this is here (using-xpath-with-default-namespace)