Generally, if you have to ask then, yes, you need permission. Just because no one is currently logged in to a server doesn't mean the server isn't running a dependency for something more important or there is a cron/scheduled task that is critical to operations.
Does this company have a change control and incident management process defined? If they do you then you should follow that process or consult with those responsible for its implementation.
What environment is this server in? PROD? UAT? QA? DEV?
You should always assume rebooting or halting a server might end up killing it. Disks love to die when they stop spinning. My last job we had some servers that were from 1999... yes seriously, because the people who wrote the code running on it lost the source code and no one works there that knew how it worked. If you rebooted them, half the disks would be dead and you wouldn't be able to rebuild the array.
Aside from dying disks... I've seen people start servers or apps one time and call it "in production" without having it set up to start automatically. You should assume someone has done something stupid like that if you like your job. I've seen people let go for less.