The way I see it, there are 4 possible options from Tokyo's POV:
1. Germany conquers Russia
2. Germany obtains favorable peace with Russia
3. Russia obtains favorable peace with Germany
4. Russia conquers Germany
The Japanese meanwhile have the option of
a) stopping Lend-Lease
b) letting it through, in accordance with their prior agreements with Stalin.
Let's say they go the OTL route and let it through, in accordance with their prior agreements (so no military aid, but civilian stuff is fine):
The preferred outcome is 1). However, by not blockading, the Japanese are reducing the likelihood of this event. At best they are delaying it, meaning they will have to keep the Kwantung army at the border for longer than necessary.
If 2) or 3) occur, then balance of power considerations will likely stop Stalin from attacking them, and they can go back to letting Stalin trade through Vladivostok. The Germans OTOH won't be exactly happy with them letting Stalin off the hook.
Then there's 4).
The likelihood of Stalin leaving them alone as a thank you gift for not backstabbing him, while not exactly zero, is still very, very small. However, even in that instance, Japan is still fucked, since the western Allies will be able to concentrate fully against them.
If however they know for a fact that Stalin will attack them once he finishes off Hitler (a reasonable assumption IMO), they really are fucked. They might think they have a slim chance if they've already beaten China and the Allies and are left alone to concentrate on defending Manchuria from the Soviets. However, that requires time, and blocking LL from entering Vladivostok means delaying soviet victory and giving them the time they need.
So, again, blocking LL seems like a superior choice. What are the dangers of it though?
Stalin has 4 options:
1. Declare war immediately
2. Declare war once he's done with Hitler
3. Leave them alone, make peace with Hitler, and try and strike a deal later on
4. Do nothing since he will have been conquered
1) is unlikely since it detracts from the fight for survival against Hitler without actually being able to force a re-opening of trade
2) is really bad, but if you think its inevitable, blocking LL at least delays it
3) & 4) are good for Japan, and cutting off LL only increases their probability
So, when deciding whether to cut off LL, it all comes down to this question:
What is more likely?
A. That Stalin is so grateful to Japan after beating Hitler that he doesn't attack them
B. That the delay suffered by the Soviets through no LL via Vladivostok will be enough to allow the army to mount a credible defense when the time comes
To conclude:
IMHO, a good case can be made in favor of Japan closing off shipping in the Sea of Okhotsk. It doesn't cost them anything, and Stalin is unlikely to attack them earlier than he's ready to.
With hindsight, Japan is destined to lose whatever they do, but somehow they thought differently in '41...