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Now all but the smallest R/C ships require some extra ballasting to bring them up to scale weight. If this extra ballast were to be concentrated in the nose and the stern of the ship, might this not tend to increase the inertia of the ends of the ship and reduce its liability to pitch?
Essentially, this is correct. Not only the mass but also the mass distribution has an effect on ship motions (mass by virtue of draft). If the mass would centered in a point, it would be most easy for the ship to pitch. When we perform a test in seaway, we always make sure this distribution is correct on a swiveling table, pitching and rolling the model and redistributing the mass until it is correct. When you change the mass distribution you change the so-called the moments of inertia of the ship and you change the response. (Mass is the resistance against changing speed of an object, moment of inertia is the resistance against changing its rotation)
Generally speaking, ships do pitch upwards when encountering a wave head-on, but there is always some phase lag between the wave and ship motion. It is possible to have a ship move exactly opposite to the wave motion.