This is just MY opinion and worth everything you paid for it.
The flaps are there to smooth out the water flow from the skeg to the rudder. This is highly important if you are racing. You might need that 0.05 knots. But for the cruising sailor, not so much as most cruisers are not trying to get that last 0.01 knots out of the boat. Plus it is hard to get bottom paint into the area between the skeg and the rudder and you might end up with a few pounds of oyster reef in there.
I just had my rudder and skeg rebuilt from Hurricane Sally and the yard brought her back to factory condition with the flaps. so.....