Could cargo decks match the strength of gun decks?

Were East Indiamen's cargo decks as heavily built as warship decks carrying cannon?

Yes. The decks had to support heavy cargo, which required substantial structural strength.

An East Indiaman's decks needed to carry heavy cargo. That requirement could produce structure comparable to a warship's gun decks. Their strength therefore had a commercial explanation even when the ship carried a relatively small battery.