When did WW2 start?

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The immediate logical argument is that Vichy France wasn't Neutral. Off the top of my head Vichy and Allied forces fought in Syria, Madagascar and North Africa. The legal argument is also pretty simple, if Google has played me fair - blockade declared, any blockade runners are fair game. Check out Sweden, who knew the rules, sold goods to both sides throughout WW2 and lost a fair bit of shipping to both sides.

 

But for a period they were neutral:

"Vichy France in 1940–1942 was recognised by most Axis and neutral powers, as well as the United States and the Soviet Union. During the war, Vichy France conducted military actions against armed incursions from Axis and Allied belligerents and was an example of armed neutrality. The most important such action was the scuttling of the French fleet in Toulon on 27 November 1942 to prevent its capture by the Axis. Washington at first granted Vichy full diplomatic recognition, sending Admiral William D. Leahy as American ambassador. US President Franklin D. Roosevelt and Secretary of State Cordell Hull hoped to use American influence to encourage elements in the Vichy government opposed to military collaboration with Germany. Washington also hoped to encourage Vichy to resist German war demands, such as for air bases in French-mandated Syria or moving war supplies through French territories in North Africa. The US position was essentially that unless explicitly required by the armistice terms, France should take no action that could adversely affect Allied efforts in the war"

Well, since 1945 the UN has the say as to the legality of a blockade. However, the United States per the "The Commander’s Handbook on the Law of Naval Operations", directly addresses naval blockades, the rules the US follows, many nations have/had different protocols. "5. The blockade may not block access to or departure from neutral ports and coasts." This condition would make a shipment by Japan (neutral at the time) to Vichy France, or Spain or Portugal and its colonies legal. As a matter of practical application each nation could (prior to 1945) and often did determine if a blockade is legal or illegal based upon its own parameters. Britain had a stricter interpretation and generally recognized most blockades. The United States and France had more liberal interpretations and have historically not recognized certain blockades and declared their intention of resisting by armed force for any attempts to harass their shipping.

 

Vichy was never neutral according to Britain, who were the ones enforcing the blockade. They announced the extension of their blockade to cover Vichy quite promptly, and championed the continuation of the French government in exile (as they did with Poland and various other occupied nations). Recognition by the Axis (including the USSR at this point) is a legal fig leaf being as that bloc established Vichy, who were effectively their client state. It is true that around 40 nations did recognise Vichy because they ticked the correct legal boxes in terms of French law to become the government, even though it was all done at the point of a German bayonet (and denounced as illegal post-war!). However, Britain's relations with Vichy are.. interesting. Never formally recognised, but blockaded. Never actually declared war, but fought. As far as I can tell we assumed they were a German client and acted as such.
Portugal and Spain, no worries mate those are neutral. Biased (one either way) but neutral.

But bottom line, back in the 30s and 40s, a declared blockade meant that any ships heading into it were liable to be stopped and searched (regardless of nationality or declared destination), and any goods destined for the blockaded nation could be seized. Entirely legally. Essentially, as you said earlier, might was right in Naval law at the time.

Sweden is again a good example of someone who understood the rules. Between 1939 and 1941, as a neutral nation, Sweden desired to trade with the USA, also a neutral nation. To do so Swedish ships had to sail through waters that both Britain & German had declared a blockade over, so they brokered a deal with both those nations that established safe parameters for their ships (routes, timings, even the colours the ships were painted) to prevent awkwardness. And this was neutral to neutral trade, exactly as you are posing in your conundrum.

Another example is the admittedly hilarious multinational attempt to blockade Spain during the Civil War in order to prevent war materials getting to either side. Hilarious because the entire Mediterranian coastline was patrolled by Germany and Italy, who were liberally sending equipment and 'volunteers' to Franco, and because the blockade leaked like a sieve even where people were trying to enforce it. But for our purposes, every ship sailing through the Straights of Gibralter was stopped and searched (or was supposed to be...) regardless of nationality, destination, etc. Because that is how blockades worked, and everybody knew it and accepted it.

The people who protested about the blockade were the Spanish Republicans, simply because it did cause them problems. They even attacked patrolling warships

 

The "timeline of ww2" link appears to be dead, and the "major conferences of ww2" one comes up telling me the connection isn't private.
Might be this end though.

 

Well not to Britain but it was fully recognized by the United States, not an Axis country. How about Australia, Canada and China? it was Britain's unprovoked attack on their former allies at Mers-el-Kabir that made any further relations between Britain and Vichy France a no-go.