I do not know but I will offer two items that might be of use
first as you speculated, different guns had differing amounts of ammo,400 rounds to each of the 4 inner guns, 375 rounds to the 2 outer guns
second, and probaly the real reason, the boxes do not just sit in the wing but rather are loaded with the case lids forming a section of wing skin. Also, the boxes are all of different sizes.
so the numbering system was probably to save time and confusion with the boxes marked "1" and "3" being interchangable with other "1"s and "3"s