Subs require significantly more thrust per cubic metre of cargo.
Communication and navigation are more difficult because GPS and satellite comms don't work underwater.
Loading and unloading in comparable times to a standard container vessel.
That's a really good point, how do you get a signal to a submerged unmanned submarine under all that conductive saltwater? Military submarines use VLF radio waves that can penetrate saltwater fairly deep, but those long wavelengths require enormous aerials and powerful transmitters that are one thing if you're the navy of a nuclear power, quite another if you're a shipping line looking to make a profit.
[1] https://www.navy.gov.au/ran-aviation-history/laser-airborne-...
Nothing insurmountable, but it's not as simple as running under everyone which is what the article implied (to me atleast).
If subs are designed for cargo then unload/loading operations can be optimized.
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.