Call in advance of appointment
It may or may not be standard around the world to let visa applicants know if there might be delays in their visa processing (that is, that they might need to have a clearance done), but it sounds very considerate of the Ottawa people to let you know before you make your travel plans. There are hundreds of messages on these boards from people who had to have clearances done, but weren't expecting it. It's good that you got this information and can plan your travel, allowing for the time it takes to do the clearance.
If you decide to travel outside Canada while your clearance is being done, don't forget to apply for a multiple-entry visa to Canada. Otherwise you'll have to apply for a new Canadian visa to get back to Canada to have your visa issued.
Good luck!