It has been a long time since I've looked at the Spacemaster rules and Imperium setting information in-depth, but I suspect that what you are seeing is simply a reference to a sci-fi version of the pallet systems currently used within the shipping industry. They are simply a platform that allows easy combining of smaller items int a larger and standardized size with features of the pallet allowing for easy movement in and out of containers or vehicles. If I remember correctly (but again it has been a long time so I may be way off base here) the sci-fi version is actually similar to small cargo containers that are loaded on ocean going vessels that can then be pulled off and loaded on semi-trucks and railroad well-cars for transport.
But as far as a ship needing them I don't think it is a necessity, but it would be more convenient and provide faster loading and unloading, but the pallets themselves would not be permanent to your ship, but would be the "container" (and that term is used very loosely (and I mean that littterally) when it comes to pallets) that is loaded on the ship that the manifested cargo is contained within.
hope that helps