If you go from an official firmware release to official firmware release with no jailbreaking and such, then you never need to worry about things not getting updated during an OS update. Apps are updated individually during normal operations, but an OS update gives you EVERYTHING that comes with the new version, like it or not. I would advise uninstalling anti-virus on your phone before an update, and possibly launchers in some cases, but other than that, you shouldn't run into any problems. Anti-virus MIGHT get in the way of updates, and while launchers shouldn't affect things during the update, it never hurts to play it safe for the update, then install your launcher of choice after the update is done.