The Shutdown command does a controlled shutdown of the device's FreshTomato firmware (Linux OS). After shutdown, the FreshTomato router/device will power off. You must power cycle the router to power it back on.
NOTE: Since Release 2020.8, Shutdown will prompt a second popup to confirm the selection. This was introduced to differentiate visually from the reboot function, since the two links sit next to each other. The wrong button could potentially be clicked by mistake.