Deep water subs require serious fixed reinforcement (like gigantic periodic rings) to prevent being crushed at low depths that would stop you from easily exposing the interior for unloading - but given that they're only going 50m deep I'm sure you could have some mechanism to pop the sub in half and get all the access you need. I feel like turbulence is sort of a solved problem by way of pallet packing - but that actually raises a larger concern of mine - the sub they display is pretty tube-shaped which means it's either not going to use pre-packed pallets (definitely the case if the image shown is to scale) or it's not going to use pre-packed pallets efficiently. Habours leverage pallets to minimize the manual labour needed for loading/unloading so while the ship might open like a sardine can it's not going to see a lot of use if someone needs to lift boxes out of it one at a time.
If there are no people on board, couldn't the air pressure be boosted to match the external water pressure?
If the pressure is balanced, removing the need for a pressure hull, the sub could have a more rectangular cross section, allowing it to be packed full of regular shipping containers.
I am not sure how thick the reinforcement actually need to be in order to comfortable cover the minimum 6 atmospheres of pressure at 50m. My intuition with diving gear tells me its should not be that bad, but I don't know how much things scale with volume.
Missile subs have large vertical tubes that can quickly be unloaded and loaded with a crane. If a sub can have big missiles you can pack it with pallets of bottles