Would like to Hide report/pivot/search/Alerts on a specific app and keep only the dashboard option active
Is there a way to hide them using navigation menu xml
Go to settings -> All Configurations and find an object with the name default and remove the references you don't need.
Your navigation menu is much easier to find using Settings -> user Interface -> Navigation Menus.
settings -> All Configurations> Default has only the following stanza.
<view name="home" default="true" />
Can this not be done on a specific app instead of doing it for all the apps? Assuming this setting will change it for all the apps.
Make sure you are on the right app context to get to the right default object. Like Martin suggested below, Settings -> user Interface -> Navigation Menus is much easier to find.