Long ago I read a book "Undersea Victory: The Influence of Submarine Operations on the War in the Pacific" by Wilfred J. Holmes, but it was in Russian translation and I'm unable to find its available English version now. So there may be some discrepancies because of re-translation.
The author himself was a pretty distinguished submarine officer of the US Navy, with enough authority to regard his opinion as significant.
In the book there are first two chapters, which were written in style of novel and cover the first missions of the USS Gudgeon and USS S-38 in December 1941-January 1942, and they give some impression about everyday life on board of a submarine during the war, while the submarine was on a combat mission.
I don't remember all the details in the book, but there are some quotations I was able to find in a minute, which pertain to the subject (note, this is a re-translation from Russian):
In the high seas a submarine must be ready for an emergency dive in case of any surprise. All the hatches on the deck, except the conning tower one, must be closed and tightly battened down until a moment, when the mission was over and the Gudgeon, while returning to her base, passed that entrance buoy in the fairway [the author is describing a moment, when the Gudgeon was leaving the Pearl Harbor naval base and is talking about a buoy which seems to be marking the entrance to the base or something like that — my note]. After the submarine was ready for a dive, she and everyone, who was on her board, became as if an autonomous particle, separated from the world.
I suppose this corroborates the opinion that there usually were no leisure sun-basking or fresh air breathing sessions on the deck.
And this was true even for subs, which patrolled Japan's coast and were based at Pearl Harbor, even during their voyage from Hawaii to Japan and back, because of many dangers: enemy surface ships, submarines, but especially aircraft, as Holmes describes:
During several days the submarine could move on the surface both at night and day, without exposure to significant danger and incessantly closing on a remote combat zone designated to her; but as she closed to the Japanese waters, surely it would be necessary to exercise more caution. The Gudgeon crossed the time demarcation line and entered the Eastern hemisphere.
As she entered waters in the 500-mile radius of the Japanese air base, she, in accordance with an order of the Commander of the Submarine forces [I'm not sure, if the title was back-translated correctly — my note], had to dive at dawn and move submerged until the full darkness, so that the enemy could not spot her. It was believed, that Marcus island, located at 1000-mile distance from Japan, was a Japanese naval air base. In order to reach the designated zone of patrol, the Gudgeon had to move 1500 miles through the waters, above which Japanese aircraft were patrolling.
Regarding life of board a submarine, there are several other excerpts, which touch many aspects, but no one mentions any crew members on the deck "to stretch their legs and get some fresh air", as was asked in the referenced question:
The routine of submerged move during day time exhausted the crew.
… The crew was divided to three shifts: one was being on duty, while the two others relaxed, made small repairs, tuned torpedo mechanisms, read or worked with documents.
… The radar, water-distiller and air-conditioning system — were three big advantages of the American submarines, but the Gudgeon was dispensing with the first two.
With the air-conditioning life was acceptable on board of the boat. On older submarines, without the conditioning system, heat and humidity, as the boat was submerged during all day, exhausted the crew, slacked them and caused skin diseases. As soon as the Gudgeon surfaced and her engines cooled, the air-conditioning system, which regulated temperature and humidity in the range most comfortable for a human body, started to work. On board there were chemicals to remove CO₂ from the air … Nevertheless, when the day ended, it had become pretty stuffy in the compartments and when the boat surfaced, fresh was meaning for men the same, as a drink of cool water for one suffering from thirst. Air pressure increased during the day, but it was possible to decrease it with an air-compressor. Still in certain cases the crew tried to avoid its use, since it created high noise.
I think, this answers the question to a certain extent. I cannot recall now an example pertaining to other periods of the war (the one provided describes only its initial stage), but I don't think that instructions regarding "strangers" on the deck could have changed significantly.