Is SNMP v3 supported in Windows Server 2016?

Windows Server 2016 does not support SNMPv3. Microsoft officially states that SNMP is deprecated in Windows Server 2012 and up, so I doubt you'll be seeing anything from Microsoft in the future either. They are all into WinRM and Powershell remoting now.

We've had a similar issue a while ago. The way to achieve Windows Server SNMPv3 security compliance is described here: https://espincorp.wordpress.com/2015/06/24/how-to-achieve-windows-server-snmp-v3-security-compliance/

Did the job for us and I hope helps you too.