I have been using Java web start for my application and I know accessing the application using web url will guaranteed the most recent version but I am curious to know if there is any way we can force the java web start application to automatically uninstall the existing version and update the application to the latest version while accessing through the shortcut.
I don't think there is a way to do that. Since you are using the shortcut you are using the local downloaded copy of the JNLP file when starting javaws. You (or your users) will have to click on the 'start with webstart' link on the site to ensure that the newest JNLP is downloaded which can then include the update application jars.
We do not allow shortcuts for our JNLP webstart applications which means the users must always use the link on the webpage to start our application for this exact reason.