Yes you can send a message via the Command Prompt to a user on the network. Windows Messenger Service is known to be very flaky at the best of times, so it may well not work correctly.
Disabling the service entirely is a common procedure for security, so you may have to enable the service on all network machines to get it functioning correctly.
Other security devices such as firewalls may also prevent Windows Messenger from working.
For more information see the Microsoft site
here. The site gives you information on syntax as well as how to enable/disable the service should you need to.
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