You can either use :silent or :silent! as a prefix to any command or you can add the ‘e’ option to the substitute, which is often easier.
:%s/x/y/ge
:silent! %s/x/y/g
:silent %s/x/y/g
For more information, see
:help :silent
:help :s_flags
The information on the e flag is a few paragraphs down from the :s_flags help.