Did cargo-configured East Indiamen still have gunports?

Did East India Company ships still have gunports in cargo configuration?

Yes. Ships could have empty gunports or painted ports, so their apparent armament could exceed the guns carried.

An East Indiaman could retain gunports when carrying cargo without a full battery. Ports pierced through the hull did not necessarily contain guns. Painted ports could also add to the appearance of armament. Counting apparent openings from a distance could therefore exaggerate the weapons actually carried.