At my level, I have not turned down one. However, there are a couple of cases where I have questioned whether it should have been applied. In other words, procurements came forward and in retrospect I've said to client departments that they might have wanted to think about a national security exception in a case where they didn't apply it.
It is challenged at several levels in my department before it gets to me, so there are many instances where government departments have been told it does not apply in this case for these reasons, or there is no need. There is a robust challenge function throughout, and by the time it gets to me, I do ask several questions and perform a challenge function, but in the two years I have been there, I have not said no to one, and there about 20 a year in total.
Can colleagues add to this, perhaps?