This is an intriguing concept, but given that the submarine is small and suitable for mostly high-value cargo (whisky is the example cargo given in the article) I'm not sure how it'll offer significant advantages over other forms of transportation in practice.

Although submarines are more effective navigating through storms, one could simply wait for the storm to pass when shipping non-time-sensitive cargo, then use a regular surface cargo ship (which could be automated if desired just like the submarine). Surface ships also have the advantage of compatibility with our already-established shipbuilding and maintenance infrastructure, while a submarine would require the proliferation of new skills and tools to support it.

For time-critical cargo (where one can't wait for a hypothetical storm to pass), it's likely aircraft would be a better option for most shipments - certainly in severe storms aircraft can't operate either, but in that case the very act of loading and unloading the submarine would be hazardous as well.