Based on your description alone, I think most people would agree the car should likely have failed the NCT. But you need to understand the NCT is not intended to be a fully comprehensive test of roadworthiness. Many aspects of the test rely on a simple visual inspection carried out by a tester, issues like this are more likely to sneak past as they clear a backlog caused by the restrictions earlier in the year.
The terms & conditions you agree to in order to submit your car for test mean you acknowledge this limitation and absolve NCTS of any liability for issues that may not be picked up in the test.
You have suffered no loss and the NCTS have no duty to you to certify that your car is free from defects. I don't see grounds for a case against them. However, if the rust was as significant as you say, you may have a case against your mechanic, as it would appear they have failed to service and maintain your car in a safe condition.