Things the British could do to counteract Germans fixing their torpedo dud rate and inflicting a major shipping crisis.
1) Don't bother counterattacking the Italians in North or East Africa in December 1940. The Italians arn't going to do anything and attacking just gets the Germans involved.
2) Don't get involved in Greece either.
3) Use a fleet carrier or two for convoy cover, even if this means not doing something like the Taranto raid or reducing Malta Convoys.
4) Don't bother with trying to maintain Malta as an active forward air and sea base. It would be hard for the Axis to push into Egypt anyway through normal port and road capacity logistics issues.
5) Regardless of who is in North Africa or when don't try to take anything in Libya or Cyrencia until 1943. As long as the British hold Alexandria and Gibralter they can start the ultimate counter offensive eventually whenever they want and win.
6) Don't get too immediately worried about Vichy colonies or its Navy. Initial policy should be as long as Vichy isn't moving their fleet units between bases and are keeping the Germans out we are not going to worry if the fleet is in Oran or the West Indies. USA diplomacy can help here.
7) Once USA is in the war, you are going to win eventually, reduce bulk imports into Britain even if British manufacturing production starts to slip.
8) Be more passive in the Pacific. The risk/reward of committing major fleet units to Midway/Coral Sea/Tokyo raids/Guadacanal really don't seem worth it. If the Japanese try to invade Midway sit back and watch the Marines shoot up the Japanese trying to wade in. Rely on submarines (if the Germans get to fix their torpedo problems its only fair the USA fixes theirs too). Put a USA fleet carrier on Atlantic convoy cover duty.
I would only reduce if absolutely necessary. (Soviet Union was really only in serious danger October through December 1941, Bomber command raids and even the beginning trickle of Lend Lease help Soviet morale in this critical time even if only symbolic). From the lens of the time. I would be really worried about the Soviets in October 41 if I were the British.
1) Keep up Bomber command raids in 1941 (but reduce in 42 or later)
2) Keep up Lend Lease in 1941 (but reduce in 42 or later)
Not a bad list of counter measures. I tend to think you still take East Africa since it sits on the supply lines to Egypt, you can isolate it, and it is very hard to U-boats to work in the India Ocean. At first blush, the supplies of the cancelled operations you list probably exceed the supplies lost in the sinkings, so lets go to second order butterflies. Allies still win, but here are some things to deal with.
1) If North Africa is not counter attacked, and Malta falls (really more abandoned all but in name), then the Africa Corp does not go to Africa. These units will inevitably go to fight Russia. Much lower fighter losses to Germans in Med. Fewer supplies consumed on Italians on defensive in North Africa. Fewer ships lost as result. Fewer ships lost due to Malta not falling. If writing a TL, we now have to deal with additional issues in Russia. Little things like Panzer division losing all its tanks in sunk freighter don't happen.
2) Also helps Germans in Russia.
3) Helps Italian navy a bunch. Means you need to have more warships for Torch since these BB that are sunk IOTL might come out to play in Torch.
4) See #1, but yes, Italians will not take Egypt, especially since Africa Corp never arrives in Africa.
5) Yes, you have staging grounds. But to be fair, Torch came from USA not Gibraltar, so the rock is overstated a lot in importance.
6) Some risks, but probably does not show up as risk that becomes major issue.
7) Yes, Allies win.
8) You still fight pure naval battles. USA carriers are not great choice for Med or to sit for long near any Axis European coast in 1942.
But it gets worse. Maybe Wiking can speak to where the Germans are most likely to use the extra forces, but it will hurt Russia. We have plenty of what if based on Axis doing better, so let's go over some potential ones.
A) Extra forces focused on Army Group North. Leningrad is either totally cutoff or falls in 1941. Big help for Germans.
B) Forces thrown towards Moscow. Don't think Moscow falls, but lead recon elements of Germans could see Kremlin. Lot, Lot more damage to Moscow before they are push back. Just the effect of fight.
C) Army Group South. Less clear here, but pretty sure lines are farther east. Helps in 1942.
Ok, now Soviets still have good winter. But Germans can still attack in 1942. Probably most of the extra forces for Germans ground up over winter, but Soviet adittional losses worse. Keep 1942 plan the same. We have fewer Soviet counter attack, weaker attacks. Is 6th Army still lost. Maybe the Volga can be held in part until 1943. Also, Torch might be late. USA has to attack somewhere. Probably still does, but we have likely cut out the Italian part of the campaign. Italy stays in war longer.
Sure Allies win, but a lot of extra Allied fighters and civilians die. Not all POD's change who wins wars.