services is only used for programs that wish to connect to a port name versus the actual port number
If you have a program that will only accept connections based on port name (and not number) then commenting out lines in /etc/services makes sense
In general, it is a fallacy that commenting out /etc/services entries makes your machine more secure. Stopping an unneeded port from listening is the only true way to close up security on that specific port.
When changing default ports, be aware that not all clients can handle that change, and they may need to have their client-side configs changed as well