One of the things that often gets overlooked is the cooling systems on shipping container homes and its one of the reasons that puts many people off having one in hot climates. But if you take the picture above you can see the utilization of several natural ways to cool a building.
A- Is using a ducting system to allow hot air out and cold air into a building which could be utilized on a multiple stacked container home by adding ducting to the exterior rear of the building. You will also notice they have added ceiling ducting to help drive the hot air out.
B- As hot air naturally rises you can see from the sketch that creating a vent at the tip of your secondary roof (adding a secondary roof to shipping container homes drastically helps reduce heat build up as it provides shade) helps let the hot air build up out but even this is assisted by the ventilation ducts to help keep cooler air running along the inside of the roof.
C- The one that may seem obvious but I haven’t seen utilized in most of the designs I have seen is vented windows. As you can see the cool air flows into the property while the hot air travels along the ceiling and out.
These may not be ideal solutions in all locations and due to the extra costs of installation I would look at the general wind conditions of where your planning your container home and if this technology will work for the property or not. Another idea if very “breezy” for cooling is using the pitched roof for gathering cold air and forcing it into the property at a low level and thus allowing full use of the roof space you install for cooling.