So I guess in order to answer the question we need to know what was submarine warfare policy around 1936 did it rely heavily on the element of surprise and if so why was such an article added, was it just wishful thinking or did creators of the treaty really believe submarines would operate in a stop and search manner?

There are multiple sides to submarine warfare in this period.

We are all quite familiar with the use of submarines against merchant ships, this has become by far the most common version of the story told. But there is more capability for submarines than simply attacking merchant ships. A good summary is found in this postwar US report on Japanese Submarine Operations:

A. Missions with the Fleet During Operations

1. Tactical Scouting

2. Screening

3. Reconnaissance (including using submarine-launched aircraft, which the Japanese emphasized more than most)

4. Ambush

5. Fueling Planes

6. Air-Sea Rescue

7. Anti-Air-Sea Rescue

8. Minesweeping

B. Contributory Missions Under Control of the Fleet

1. Surveillance of Allied Ports

2. Mining

3. Attack on Supply Lines (i.e. merchant ships)

4. Attacks on Allied Ports (generally targeting warships)

C. Transport and Supply by Submarine

1. To and From Isolated Bases

2. Transport of Material to Japan (mainly from Germany)

US Submarine Doctrine of February 1944 covered similar points, and US submarine operations during WWII were similarly varied. Submarines resupplied Corregidor and brought out important material, landed marines on various Japanese-held islands, mined Japanese ports (later taken over by B-29s), rescued downed US pilots (basically their only job towards the end of the war), scouted Japanese harbors and acted as pickets ahead of expected Japanese advances, gathered intelligence on Japanese bases, bombarded Japanese islands with their deck guns, Barb even launched rockets against Japanese cities and landed a shore party that blew up a train. Oh, they also attacked merchant ships.

The doctrine heavily emphasized the use of submarines in areas outside attacking merchant shipping. I'll trust you to read Chapter 1 and Chapter 3 of the US Doctrine (they're short), but you'll see the focus is not on attacking merchant ships, but on other missions. Attacks on shipping are of course mentioned, that's part of the role for a submarine, but as you can see they are emphasized far less than the other missions.

Thus, during WWII, the focus for submarines was, according to the manuals, mainly against military targets, not merchant ships. The information I have suggests that, in most respects, this was little changed from the manuals of ~1936.

However, there is one clear change evident in Chapter 3. I have emphasized the relevant lines.

Patrol against enemy lines of communication includes the destruction of commerce. It may be expected that the convoy system will be used, especially at focal and terminal points. On the high seas, circuitous routing will be employed. The torpedo is the major weapon in these operations, as the submarine is not equipped with gun power to equal that which may be expected on modern merchantmen. The submarine gun may be employed against vessels known to be unarmed or small vessels of minor resistant qualities. Operations in the vicinity of focal and terminal points will produce more targets, but the intensity of anti-submarine measures will also be increased. The principles of the submarine attack against commerce do not differ from those used against other types of vessels. Submarines operate singly in assigned sectors on the edge of focal and terminal areas and furnish information of enemy shipping to other submarines similarly employed. Submarine positions should be shifted frequently to cover variations in shipping routes as well as to evade concentrated anti-submarine effort in areas of operations discovered by the enemy.

By 1944 when these instructions were published it was clear that surfacing to engage a merchant ship in daylight was a risky business (night surface attacks, however, were very common during the war). This was even evident in WWI, which led to trouble with German U-boat activity at that time, which many considered barbaric. However, the issue was contentious: as Parks discusses, there were "[n]ear, continuous negotiations between 1919 and 1936" on this subject, with Britain even arguing the submarine should be abolished. I am not going to try to summarize the debates in detail other than to say each nation had their own ideas of what the rules should be and getting everyone to agree was a nightmare. This nightmare created the 1936 rules that were so vague as to be useless: to name but one stumbling block, what about armed merchant ships than can sink a submarine?

Parks summarizes the position of the major submarine powers on this point during the war. Germany began by following the 1936 rules, with some exceptions like troop ships and convoys due to the ambiguities above, but Dönitz and Hitler relaxed those standards during the war. Italy followed German rules once they joined the war. Britain followed the rules until 1940, when they too began relaxing the restrictions in certain zones. Japan never agreed to these terms. And on 7 December 1941 the US immediately ordered unrestricted submarine warfare in direct defiance of the Procés-Verbal, and while the date would place them after the other powers, unlike the European navies there wasn't even lip service to restrictions for certain zones. Parks then elaborates on how the various commanders within the US Navy expected unrestricted submarine warfare well before the war, which emphasizes the disparity between the politicians and the commanders.

Thus to answer the question "did creators of the treaty really believe submarines would operate in a stop and search manner?" should be answered yes, probably (hard to read minds), at least for the diplomats creating the treaty. They certainly believed some merchant ships would be immune, largely due to the differing definitions of "merchant ship", but their beliefs did not agree with other nations or even their own naval officers. Thus, were you to rephrase the question to "Did the signatory nations really believe submarines would operate in a stop and search manner against all merchant ships?", that changes to "depends on who you ask".

Park's paper then moves on to discuss lessons for modern treaties, but his opening is a good summary that highlights the division:

In a war that saw each and every major submarine power consciously abandon the rules in the 1936 Procés-Verbal, it is an understatement to say that the treaty did not measure up to the harsh reality of war. Its postwar status has been debated,^(162) as has the legality of exclusion zones by whatever euphemism they may be called.^(163) Even the most ardent defenders of the Procés-Verbal provide numerous clarifications and conditions identified by submarine officers before World War II but persistently ignored or dismissed by diplomats, negotiators, naval leaders and international lawyers of that era.