Não há diferença neles. Internamente, eles fazem exatamente a mesma coisa:
1. reboot uses the shutdown command (with the -r switch). The shutdown command used to
kill all the running processes, unmount all the file systems and finally tells the
kernel to issue the ACPI power command.
2.init 6 tells the init process to shutdown all of the spawned processes/daemons as
written in the init files (in the inverse order they started) and lastly invoke the
shutdown -r now command to reboot the machine