Why did Japan fail to interfere with shipping from America to Vladivostok from 1941-1945?

I think I found the answer. The Second World War was a war for hegenon between Eurasian powers such as Great Britain, Germany and Japan. And the United States and their political golem the Soviet Union. This war took the form of Hegelian dialectics. Such a process required the installation in all countries of a very influential agency, often acting as the ruling elite. These elites pursued policies that conflicted with the interests of the countries they managed. A good example is Adolf Hitler or Hideki Togo. The result of World War 2 was the acquisition of world hegemony. This required the destruction of Eurasia.

Japan had a five year non-Aggression Pact with the Soviet Union (which the Soviets broke in 1945 after four years). Attacking Russian shipping would have been an act of war, and Japan didn't really want or need a "third" enemy. Japan feared that the Americans would use Soviet territory to launch air strikes or "stage" an invasion if it provoked Russia sufficiently. In this instance, therefore, Japan was content to "let sleeping dogs lie." The country did have the consolation that the materials would not be used against her (at least until the 1945 "double cross.")

Yes, Japan was allied with Germany, but only against England and the U.S., the two maritime powers that Japan truly feared (and were capable of invading Japan). The book "Marching Orders" and other sources show that Japan urged Germany to make peace with the Soviet Union so they could concentrate "two on two."

Why should they?

Destroying those supplies would require the commitment of forces Japan did not have to spare, with little to show for it.

If a country Japan was at war with -- the USA -- insists on shipping war supplies to a country Japan was not at war with, why should Japan mind?

Whether those supplies reached Russia or not did not make a difference for Japan. (Except perhaps merchant tonnage sunk, but the US was more than capable of replacing such losses.) They could instead try to sink supply ships supplying US troops, which would be much more useful to Japan's war effort.

In addition to the points already raised by @TomAu and @DevSolar...

The Pacific lend-lease route skirted the problem by officially being handled by the Soviets. Supervision and routing was handled by the Soviets. Cargo was loaded into Soviet flagged ships, many US ships were handed over to the Soviets. Since ships on the route might be inspected by the Japanese they did not include war materials. The Pacific route handled things like food, trucks, and locomotives which were allowed. War material instead went via the Arctic Convoys and the Persian Corridor.

Attacking the US/Soviet lend lease would have meant sinking Soviet ships killing Soviet sailors and loss of goods purchased by the Soviets. Since Japan was not at war with the Soviets, and was anxious to not be at war with them, there was little justification to attack their ships.

There's an insinuation in the question that Japan could simply attack the Soviets, and there was nothing the Soviets could do about it. The Japanese had already learned this was not so.

Since 1931 the Japanese had been testing the Soviets in a series of escalating border skirmishes. In the summer of 1939 this escalated to a major battle, the largely forgotten Battles of Khalkhin Gol. Then Corps commander Georgy Zhukov was called in to deal with the Japanese probing attacks once and for all and show what the Soviet army was capable of when it got its act together. Zhukov used massed armor to achieve a double envelopment to decisively end the battle.

After this humiliating defeat, the Japanese attitude towards expansion switched from looking north at Siberia (Hokushin-ron) to looking south at southeast Asia and Pacific islands (Nanshin-ron). The Japanese had already suffered a defeat the hands of the USSR, and now had no motive to pick a second fight by interfering with their shipping.