The WHM panel provides two options for a server reboot:

Forceful Server Reboot
Graceful Server Reboot

The recommended option is Graceful Reboot. This way the reboot will be queued, and when all services are stopped the server will be restarted.

In a case there is a very high load on the server, the Graceful Reboot might not be sufficient. Then you will need to use the Forceful Server Reboot option.