I think most players use the hovercraft as a car, for transport and storage of the materials that they usually don't carry in their inventory. Like mines, or rails, or walls, or whatever. Both can't be automated, so I don't really see the harm in allowing them the same inventory size.
"Emergency storage" would be those items that you need to take along with you after demolishing a section for example, but wouldn't fit in your inventory.
With the hovercraft basically replacing the car, because we need to travel between islands, the lack of that extra storage space has become an enormous hassle to do the manual things that we normally do. Like building up defenses, or reorganizing your structures.
I don't think anyone was using the hovercraft to transport large amounts of containers on a structural basis. Sure, it happens once or twice, because of those emergency cases, where you tear down something to rebuild it somewhere else, but not as a reliable or easy method of supplying your factory.
I feel the decision to remove the inventory slots does not add to the intended "freight-workings" of the mod, but hinders players in organizing their work to make those intended workings happen.
Just my 2 cents. I love everything else about the mod. Got over 200 hours in it now. The boat is fine at 6 slots, but I especially love the hovercraft with its crazy drifting ability and frankly, crippling it by taking away its trunk was just cruel man. ;)