It all comes down to the grand battle plan the Japanese had for WWII... that of The Decisive Battle (or Kantai Kessen). Unlike War Plan Orange, the US plan for a war against the Japanese which covered "island hopping" and an extended campaign, the Japanese had planned to end it all in one final stroke.

The Japanese plan went something like this:

War was declared for whatever reason. The US Navy's battle line would sortie out from the West Coast (later Pearl Harbor). Japanese submarines would act as scouts to keep track of the Americans, and pick off the occasional warship here and there, weakening the force. Land-based air and light warship units would similarly bite the ankles of the US Naval force, weakening them even farther. Then would come the one massive battle between a fresh Japanese navy and a bruised and tired US Navy, in nominally Japanese waters (originally the Ryukyu islands south of Japan, ). In the glorious tradition of the Battle of Tsushima, the Japanese fleet would smash the Americans, with their submarines picking off the cripples and retreating ships.

This strategy, which was modified somewhat as aircraft carrier technology improved, is what the Japanese sub force trained for... they were basically designed and programmed to go hunting for warships. If you think about it, even their most famous weapon, the Type 95 torpedo (adapted from the Type 93 torpedo launched from surface ships, the so-called "Long Lance"), was designed to kill warships... you don't need long range and a huge warhead to sink a 10000 ton freighter, but they do come in handy when you're trying to open the side of a battleship.

Certainly they could have gone after shipping in general, and in retrospect they obviously should have... a handful of Japanese subs stationed between Pearl Harbor and the West Coast ports could have raised holy hell with the logistical situation... but that's not what they planned for. One even gets the feeling that sinking freighters was beneath the notice of Japanese submarine commanders.

By the time anybody gave thought to a sustained offensive against merchant shipping, the US Navy had learned the tricks of the anti-submarine trade in the crucible of the Atlantic. The adventures of the USS England in 1944, using the British "Hedgehog" system created during the Battle of the Atlantic, are telling.

It seems safe to chalk this up to yet another missed opportunity caused by a focus that for the IJN could be somewhat narrow and inflexible.

###Section 1 - What is unrestricted submarine warfare

Let’s clear something up “unrestricted submarine warfare” simply means that warnings are not given before an attack on a merchant ship. The Japanese did attack Allied ships without warning and there are plenty of examples of this around the Australian coast and if you don’t want a short explanation of prize rules skip over to the next section on WW2 in the Pacific.

These warnings are dictated by prize rules which have their own history developing out of British Prize courts but for our interest in submarine warfare in the 20th century restricted submarine warfare basically means that it abides by Article 50 👀 of the London Declaration concerning the Laws of Naval War.

Which states—

Art. 50.

Before the vessel is destroyed all persons on board must be placed in safety, and all the ship's papers and other documents which the parties interested consider relevant for the purpose of deciding on the validity of the capture must be taken on board the warship.

All of this is well and good, it has historical precedence in how states behaved in the age of sail, in 1909 your main raiding force would be “cruisers”. For people who don’t know your naval ship types cruisers are smaller in displacement than a battleship and around the advent of the dreadnought the main naval doctrine of major powers was to have a main battle fleet of pre and actual dreadnoughts at home and separate forces of armoured cruisers who were tasked with colonial policing and trade protection. So they are large enough ships so have space, food etc for captured crew and are quite large warships themselves so aren’t at risk doing this unlike submarines.

The voyage of the Emden is a excellent example of “Cruiser rules” being followed, but outside of a small isolated number of such exploits the experience of World War One was that surface raiders could be eventually dealt with or otherwise bottled up on port. And submarines who had not been intended in the commerce raiding role solely found themselves better suited than cruisers due to their stealth, however they had substantial problems with following article 50. Submarines have limited space and taking on the crew of sunk vessels would require them to find a way to return them to safety or take up precious space and crew time guarding them on what are already very cramped smelly vessels with small crews.

Surfacing, giving a warning, transferring the captured crew also presented a number of risks not just from Q ships, you had a number of merchant captains who tried to ram submarines. Time on the surface and giving an enemy merchant ship time to radio in your position, at worst it’s a danger at best enemy shipping can reroute to avoid you.

All of this is to say cruiser rules were unworkable for submarines in naval warfare, now regarding the Japanese as I said at the start they did attack Allied ships without warning what I suspect your question is really asking is why was commerce raiding not a more prominent factor in the Japanese Pacific campaign.

Apologises if I misinterpret here,

###Section 2 - Japanese grand strategy and Subs

So to simplify a very complicated but important related topic, I would say that the strategies that countries choose to embark upon both in when they decide to go to war and how they conduct that war is driven by some sort of worldview. All states have different groups with different views in interwar japan one major influence in driving Japanese foreign policy in the interwar period was “Totalist” thinking. Totalists viewed limited wars as possible, and due to japans inferior economic position they believed that the best way to safeguard the state was limited wars on the model of the Russo-Japanese war and the Sino-Japanese wars of the late 19th century where by an enemy would have territory seized by a decisive battle and then the cost to regain the territory in total war would be made so high even if their economy was better that they would come to terms.

Within this grand strategy Japan can’t win a submarine/commerce war it will always be out built. Therefore submarines have a tactical not a strategic role, they are therefore trained for and deployed to strike decisive blows against enemy fleet units or supporting the Japanese navy to carry out a decisive battle.

###Section 3 - A comparison with the Atlantic

I’d also make a point regarding the German u boat campaigns commerce raiding needs to be focused against an enemy with a large dependency on imports for war materials and/or food. This is true or Britain and Japan but not so much for the US but you can argue there are two combatants who are dependant in war materials in the Pacific. Namely Australia and China.

Regarding China Japan had seized all of the major ports by time of war with the US so the supply route is via British India and “the Burma road” it doesn’t make sense to risk transiting the Pacific with this. And with respect to Australia you supply routes are in the South Pacific, and in fact the Guadalcanal campaign was fought by both sides to get bases to protect/interdict this route.

So a major reason for the disparity in commerce raiding between the Atlantic and the Pacific was that the Atlantic had a lot more shipping and its passage into Britain was within range of bases in Germany, Norway and France. The Pacific is much vaster and during the war there was less commercial shipping and where there was shipping it wasn’t the easiest to get at.

Here is an interwar map showing major trade routes and you can I hope see what I’m talking about the Atlantic is much busier, and also smaller.

[FYI I’m not a historian, just a buff I hope this was alright]