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Many times you have to check bending moments and shear forces when cargo is loaded because if a tank is full or partially full the effect of cargo + liquid can exceed the allowable moment or force.
Another times an empty tank is needed due to free surface effects. If the capacity is, for instance, at 50% the stability is reduced and instead of consume fuel of another tank you have to empty that tank for minimizing the FSE.
As my knowledge that it must to have a tank with water not completely full which called a ballast tank is a compartment within a boat, ship or other floating structure that holds water, which is used as ballast to provide stability for a vessel. Using water in a tank allows for easier adjustment of weight than stone or iron ballast as was used in older vessels. It also allows for ballast to be pumped out to temporarily reduce the draft as well of the vessel when required to enter shallower water.