I was looking into how flags of convenience work today, and was struck by the small proportion of merchant shipping controlled by major naval powers, and by how contemporary debates about the practice seem to revolve around labour conditions and safety standards rather than strategic concerns. While I've not found any historical figures on shipping ownership, the trend seems to date back to the mid-20th century. Especially during the Cold War, it seems odd that there wouldn't have been any public debate - let alone action - about letting shipowners use flags of convenience to potentially avoid wartime obligations. If not, when, when did shipping cease to be of strategic concern?
Flags of convenience were in use during WWII. The Panamanian registry had been opened in 1916, joined shortly afterwards by Honduras. Both registries were used mainly by American-owned companies hoping to reduce their tax burden. Between the start of WWII and American entry to the war, the American government would actually sanction transfers to the Panamanian registry. Doing so acted as a work-around to the Neutrality Acts - these prohibited American-flagged ships or American crews from entering ports owned by belligerent nations. Panamanian ships were under no such restriction. While Panama never entered the war, many Panamanian ships were attacked; 76 were sunk by German submarines, along with another 11 Honduran ships. Four more Panamanian ships were sunk by German aircraft on the Arctic convoy route. These losses show why the use of flags of convenience were not considered a serious issue. While the ships may not be based in the US or the UK, the companies that own them are. As such, considerable pressure can be brought upon these companies to ensure that they use their shipping in the interests of the nation. The USA also, under the Merchant Marine Act of 1936, maintains the right to requisition or purchase any ship owned by citizens of the USA. Meanwhile, there is no risk that the countries of the flags of convenience will exert control over the ships under their flag. In the case of Bermuda, where many British-owned ships were and are flagged, this is impossible because Britain controls Bermuda's foreign policy. In the case of Panama, Honduras or Liberia, these countries do not have the port facilities to support and maintain the fleet of ships under their flag, and nor do they have the capability to prevent Britain or the USA assuming control over ships under their flag.
Following the war the War Shipping Administration was stood down and the parent organization returned to the fore for regulation, subsidizing, and maintaining those ships the govt had paid for and more generally the US civilian shipping fleet at large. This group, the US Maritime Commission did everything from running the US Merchant Marine Academy, to subsidizing loans for construction of ships, to running the new huge mothball fleets of excess shipping, and selling or scrapping hulls no longer considered needed.
The agency was then split in 1950 into the Federal Maritime Board/Commission that handled regulation of things like safety standards, pay, conduct and such. And Maritime Administration that handled funding and subsidizing construction, and running the Academy. They also got control of the National Defense Reserve Fleet of mothballed ships.
The military also consolidated their shipping organizations into the Military Sealift Command, first by transferring everything to the Navy in the late 40's, and then in the early 70's growing the organization to uses civilian crewed ships to directly support the fleet at sea in addition to normal point to point transportation. Hence why most auxiliaries in US service like oilers and sustainment ships are prefixed as USNS not USS.
But the pool of ships did continue to shrink, both the US Merchant Marine pool of flagged ships at-large. And the reserve force in the NDRF. Down from nearly 3000 ships at its peak, with crisis an wars in the 1950's seeing 100's of ships activated it has only ever gotten smaller, and older ships continue to present pressing environmental concerns. To break toe 20 year rule today there are only about 100 ships held in mothballs, about half of those are held in a state of greater readiness as the Ready Reserve Fleet, and some of the remaining are slated for disposal. That is barely 1/3 of what those numbers were even in 2000, while the RRF was similarly sized, the total pool of ships on hand if needed, along with older naval combatants on hand for reactivation as well, was much larger. https://www.marad.dot.gov/wp-content/uploads/pdf/i171231.pdf
But even with newer more capable ships and a smaller military and Navy to support the numbers are plenty alarming in many circles.
And frankly the answer is in part, it isn't a glamorous line item, and never quite got so bad as to really hamper the ability of US forces to surge forward, or global trade to help be stabilized with more hulls. In part because many of those WW2 or immediate post war hulls were still around, but as they finally ended their lives and fewer ships have been built and even fewer been on hand in any capacity for a US govt agency things have gotten much worse. Even during Vietnam there were still 100's of older ships to draw on sitting at anchor around the nation but as the environmental damage, cost, and capabilities of those ships to meet the need have shifted and that reserve disappeared with it, only accelerating post Cold War.
I would point you as an example to a recent GAO report just on the capabilities and adequacy of the 100ish ships of the combined Surge Force(Maritime Admin transports and MSC USNS transports) and MSC fleet support vessels(oilers and ammo ships and such). Obviously past the 20 year mark but does show how the discussion is going . https://www.gao.gov/assets/690/686733.pdf
Especially during the Cold War, it seems odd that there wouldn't have been any public debate - let alone action - about letting shipowners use flags of convenience to potentially avoid wartime obligations. If not, when, when did shipping cease to be of strategic concern?
A bunch of factors come into play as to it isn't a major concern (that doesn't mean it ISN'T a military concern - rather that it IS being handled):
As of June 2014, 24 carriers and 553 aircraft are enrolled in CRAF. This includes 517 aircraft in the international segment with 391 in the long-range international section and 126 in the short-range international section. There are 36 aircraft in the national segment. These numbers are subject to change on a monthly basis.
Moreover, we DO have a relatively recent historical example of an overseas war with a massive use of the modern military logistics system: Operation Desert Storm.
So from the start of Operation Desert Shield after the Iraqi invasion of Kuwait in August of 1990, the US military did activate a lot of its contingency forces to support DOD logistics requirements that ultimately moved and supplied a force of over 700,000 American soldiers, sailors, marines, and airmen - all to the other side of the world - and got them combat ready by January of 1991.
Short of World War III breaking out, I think you'd be hard pressed to find scenarios that would necessitate more than what was already accomplished and is still available.