Do Hyper-V Virtual Machine Guest Operating systems need to be shut down before restarting Windows Server 2012 R2 they are running on?

It depends on how your configured your Virtual machines.

If you have your VMs configured to 'Turn OFF', then shutting down the host OS would be close to equivalent to pulling the power from the VMs. If your VMs are configured this way, and you want them to safely shutdown, then you need to shut them down first. You could also use the other options like suspend, or shutdown the guest OS.

Do keep in mind that the shutdown the guest, requires that you have guest additions properly installed on the guest. I believe without them, you will have the 'turn off' effect, but I am not certain.

In my tests, no, the VM's do not need to be shut down. I actually tested this by having notepad open on a VM, with unsaved text, then restarted the host.

The VM came back up with the notepad open, with the text there.

I think under HyperV settings there is a default option to 'do this to VM when restarting'

I prefer to go through the process of shutting them down individually through the management console. While fairly rare, there are times the VM state has an issue or won't shut down properly on it's own. This gives me a chance to make sure all of this happens in the manner that I expected. Not to mention, there are times that the VM itself doesn't always release RAM depending on what systems are running on it, and while often it doesn't really do anything, it makes me feel better for some reason.