My belief is that only one container should be on at any given time, and that it can generate the field that would protect the vessel. If you want to have others to turn on, do so to restore your shields instead of trying to bring the old container back to life. Almost like shield projector-capacitor units with limited lifespans; once a container's field is defeated, just bring up the next container as fast as you can to restore your shield.
There is the potential for OP there, as you could really outfit your ship for whatever circumstances, but I'd like to see the container's shielding be only so good and a predictable time it takes to rev up the next container. Not to mention that once you're out of containers, you're permanently out of shields protection.