Why containerized missiles disrupt ship stability

Could a merchant ship stack containerized missiles in layers and launch them one after another?

In principle, but container weight and balance management make the arrangement difficult and conspicuous on a real cargo ship.

Container ships depend on careful weight management and automated planning to remain safely balanced. An unusually heavy or light missile container can stand out during cargo handling. Concentrating missiles high in the stack also creates structural and stability constraints that an ordinary container plan is designed to avoid.