How can I stop a message (displayed via drupal_set_message()) from being printed?
I admit to not having used it before but the Disable Messages module looks like it would do the trick:


  Gives a site owner options to disable specific messages shown to end users.
  
  Features:
  
  
  Filter out messages that match a full text string exactly.
  Filter out messages that match a regular expression.
  Permissions to specifically hide all messages of a given type from any role.
  Disable all filtering for specific users.
  Disable all filtering for specific paths.
  Apply filtering only for specific paths.
  Debug system to get messages in the HTML without showing it to the end users.
  


I think a regular expression would probably be best for this particular message (because of the replacement done using t()); something like this should work:

^Location taxonomize: [0-9]+ new terms saved$