You can use the
ManagerManager plugin to control the default values of document variables.
For example, to disable the "Show in menu" option you could could set up a rule:
mm_default('hide_menu' , true); // Set the 'Show in menu' option to false for all new documents
or:
mm_default('show_in_menu' , false); // Set the 'Show in menu' option to false for all new documents
If you don’t want that to apply to all new documents, you can apply the rule to specific templates.