As a general rule, container ships are unloaded tier-by-tier, breadth-first if you will, not shaft-by-shift (depth-first), so this is not much of a problem in practice.
That does start to change if you want to do simultaneous loading and unloading operations, then you'd want to clear out a vertical shafts first so you can start loading operations as quickly as possible. Which is one of the many reasons dock workers hate that style of operations.
As a general rule, container ships are unloaded tier-by-tier, breadth-first if you will, not shaft-by-shift (depth-first), so this is not much of a problem in practice.
That does start to change if you want to do simultaneous loading and unloading operations, then you'd want to clear out a vertical shafts first so you can start loading operations as quickly as possible. Which is one of the many reasons dock workers hate that style of operations.