Mike,
The rule doesn't limit how many rudders the boat carries onboard, it limits how many they can use overall.
I can see there being a limit on how many rudders they use overall because damaged rudders are slower than brand new rudders. Just like there is a limit on how many sails they can use overall. There is a strong resource allocation component to the race. They can't just build a new boat for each leg, even if they got the money and will to do so.
Big difference between replacing the whole boat vs. the rudders.
Several things have been challenged in protests during this running (with no penalty). I just can't see them penalizing for this, especially at this stage of the race, with the points so close. Would be completely suicidal for relations with fans of the race.
Just my two cents anyway...
Mike