what is the best method to reboot F5 LTm

There's a few ways.

GUI - System - Configuration - Reboot.

Else, from the command line I would either use the reboot command or "shutdown -h now" (this will halt and shutdown the BIG-IP). So, to clarify I don't believe you need to Halt the system if rebooting via the command line or GUI.

Finally there is the LCD display - here you would Halt the system first before powering off or rebooting.

Hope this helps, N