The Estonia had a draught of: Draught 5.60 m (18 ft 4 in).
A ship's draught is broadly
Wärtsilä
Basically, the height of the hull.
Now according to the JAIC:
wiki
So, it is readily apparent that the highest wave, would permeate (go over the deck) at 0.20m, or about 8 inches. By far the majority of water hitting a ships deck, simply washes off. The hypothetical 8 inches that may or may not have ingressed the top of the car ramp, presumed by the JAIC to be ajar at the top would only slow flood the car deck, which in turn had scuppers to release excess water, rather like a drain. In addition, as soon as the vessel turned to port away from the on coming southwesterly waves, if the car ramp was open, any water would simply wash away.