Yes, vessels are allowed to traffic at night in these restricted areas. There is no prevention.
What they are restricted to do is related to speed. When there are whales that are identified, the restrictions are put in place, monitored by Transport Canada, and any vessel that goes outside of that speed for any more than 95 seconds is automatically notified and a contravention is issued and sent to Transport Canada for follow-up as the regulatory body that is responsible for that.