Once the shutdown is done properly, all file systems are unmounted (umount'ed indeed). The root file system is turned into read-only mode. For each filesystems including the root, a clean flag is set. This flag is checked at next boot to decide if the each filesystems do need a torough check before completing the boot process. This insure that at least the structure of the filesystems is usable after a hard crash (power failure for one). It does not protect from data loss: A clean shutdown is always a good thing.