Retire 2015,
Most airline performance figures for runways in the vicinity of shipping make some allowance for shipping, both for the approach and for takeoff. For example, one airline I know use a figure of over 200' for shipping in the channel at Boston. Where the height of the shipping exceeds that figure, some other form of correction may have to be applied.
It is possible that where the airline use centralised performance determination i.e. a flight despatcher, to determine takeoff data, the pilot has no way of knowing what consideration is being given to shipping off the end of the runway.