Looks like cardboard boxes can be upgraded in Metal Gear Solid V: The Phantom Pain, going by a recent tweet by Hideo Kojima. The box on the picture below has been strengthened to increase its durability. It is quite possible that this is one of several ways to upgrade your boxes.
“The support box made out of carbon box for sending during the mission got strengthen as to increase of its durability.”
According to Kojima, you can’t rely on the paper cardboard’s durability in bad weather, which is why he upgraded it. Though the weather does seem fine on the picture, but better safe than sorry, right?
Source: Hideo Kojima Twitter, JunkerHQ