Any icon pack (not themes like Cyanogen Mod themes for example) can only apply to launchers and apps not the androidAndroid system itself.
(exceptExcept that the system supports icon packs which is not common in official ROMs.)
And Nova launcherLauncher (like most launchers if not all of them) only displays the home screen and the app drawer, anything other than that (like recentsrecent apps, notifications, and lock screen) is controlled by the androidAndroid system not Nova launcherLauncher.
Note:The The lock screen icons can be changed by a lock screen app but not Nova launcherLauncher.
Final answer: You can change the icons everywhere in your phone (CM13) if it has a theme engine and you install & apply an icon pack that is compatible with the theme engine or apply a compatible theme with the desired icons. (noteNote that you need to choose to display system icons from Nova launcherLauncher afterwards.)