I (probably as many others after the update for reward collection at the end of the missions) asked about the drop rates for item and fortune boxes.
The reply was that the drop rates were not changed and that it has been checked several times.
But as everyone else has experienced it ever since that update the boxes drop far less.
So if the drop rates (as in percentage for an item box to appear from the rewards) has not changed I can only imagine that to be because of the change in mechanism on how rewards are collected.
Every reward box needed to be opened manually + more item boxes dropped.
Reward boxes are automatically opened, content gathered and collected at once at the end of the mission + less item boxes dropped.
So my suspicion is before the update the chance to get an item box was activated for each reward box when you opened it.
Now after the update the chance to get an item box however would be initiated only once at the end of the mission when you collect your gathered loot.
But that is just my own suspicion because I believe there must be an explanation for the decreased amount of item boxes appearing from mission rewards.