Oak was the default wood for chests in the middle ages, with walnut in second place. Soft wood joinery was quite rare.1 So it was harder to work, so what? Labor was cheap and materials and furniture were valuable. Saving man-hours as the most important issue is a very modern idea. In any case, shipping container is a bad analogy, the MitD's box is more like a wooden cage or a large treasure chest than a modern pallet-bottomed crate.

1. Eames, Penelope, Furniture in England, France and the Netherlands from the Twelfth to the Fifteenth Century, (London: Furniture History Society, 1977)