Imagine this, suddenly you find your configuration manager missing. Pretty annoying and can be one of those things which can give that 15 minutes of extreme irritating moments. Not sure, why it happens ( Windows update perhaps ? ) but have seen this in couple of machines now. You can find it at "C:\Windows\SysWOW64\" directory
For SQL Server 2017 it is : C:\Windows\SysWOW64\SQLServerManager14.msc
For SQL Server 2016/2014 it is : C:\Windows\SysWOW64\SQLServerManager13.msc / SQLServerManager12.msc
To add it back to the start menu, copy it from the original location provided above and paste it to
C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Microsoft SQL Server 2017\Configuration Tools\
This would put back the configuration manager under start menu. Hope it helps!!!