Especially during an update. I don't want a shortcut on my desktop, and neither in my start menu, as i've got evernote pinned to my taskbar, a shortcut anywhere else is wasted space that makes my pc more messy.
So to recap: An option to decide whether or not to install a shortcut on the desktop and in the start menu. During a program update, do not recreate the shortcuts (because if they are not there, they have been manually deleted).