How have they traditionally handled safety on submarines in regards to "surface cruising"?

Something IMO even more morbid happened on a Russian submarine in 2015. The article is in Russian, sorry, didn't find a translation.

Submarines have a compartment that's inside the submarine but outside the habitable inner part of the sub; that compartment does not preserve air pressure when diving and is separated from the rest of the sub by a hatch that can be open only from the inner part of the sub. A petty officer went there to throw away garbage, and lingered to call his wife regarding their daughter's wedding plans. Before he could return somebody sealed the hatch and the sub started to dive. The petty officer knew he wouldn't survive the dive and told his wife as much; unfortunately, his wife had nowhere to call to reach the submarine bridge to interrupt the fatal dive.

The article goes on to describe that there are indeed protocols to prevent that, but multiple officer didn't follow them. For example the officer responsible for accounting where the men are in the beginning of the dive couldn't locate the petty officer, but just assumed that he's just sleeping somewhere. However, those officers managed to avoid criminal responsibility for that.

In wartime lookouts were sometimes deliberately left on deck when the submarine came under attack and crash-dived.

One such incident was the German submarine U-68 :

Suddenly, the siren was sounded for a crash dive. The survivor helped secure the 3.7 cm. gun and then noticed that one of the gunners had been wounded. He struggled forward with the wounded man, attempting to bring him into the boat.

As they approached the conning tower hatch, it was slammed shut and the U-boat began to submerge. In a moment, the two men were in the water, pulled under by the suction, but clear of the U-boat. The survivor, whose life jacket had been punctured by some bullets and was comparatively ineffective, remained with the wounded man for some time. The latter, wounded in the stomach and leg, had turned very pale and was unconscious. The sole survivor stated that two planes came over after he had been in the water a few minutes and dropped more depth charges; finally one of the planes dropped a rubber boat. The survivor lost consciousness shortly thereafter from the effort of supporting himself and the wounded man in the water.

The wounded man died before being rescued, the submarine was sunk, so the sole survivor of the submarine crew was the abandoned lookout Hans Kastrup, so it worked out relatively well for him.

From: Wise Jr, James (2013). Sole Survivors of the Sea. New York: Naval Institute Press. ISBN 9781612513652.

Before I retired, I was an electrical engineer and rode a number of submarines in order to test sonar systems that my company had installed. Normally we stayed on board for the entire trip which was usually 4-5 days. On one occasion, a supercharger on one of the two engines literally exploded. The submarine had to immediately surface and we proceeded to limp back to port on one engine. However, at one point, we were allowed to go out on deck to get some fresh air. We were able to dangle our feet over the side. To me, it seemed like we were on a whale. To finally get to the point, while we were on the deck, there were 2 sailors in wet suits who were there in case one of us fell overboard. Also, when we climbed down the hatch, they made sure that everyone was back in before closing the hatch. So have no fear, there is no chance that someone would be left on deck while the submarine submerged.

1) Things have changed with the advent of nuclear-powered submarines since the 1960's, but WW2 submarines were small - and had a small crew. Even the largest U-boats, the Type VII and it's cousins, were only 67m (220 ft) long, and with a deck only about 10 feet wide for most of the length. They are quite a bit smaller than even the smallest destroyers, and with a much cleaner deck,as shown below for a late-war u-boat.

Type VII U-boat

Even under North Atlantic combat conditions, it is hard to imagine being on-deck without being aware of what else is happening in those close quarters.

2) Yes, there were protocols for diving.

Note specifically from (56) below: "The Commander is personally responsible for opening and closing the conning tower hatch.". The buck, very emphatically, stops with him. However (47) - "The senior man in each room reports readiness to dive to the Engineering Officer." also means it is the responsibility of every team lead to ensure no-one is missing from their station before reporting readiness of the room/team. At every stage of the dive preparation, not only is every order repeated at least twice, but every man expects to be notified, and aware, of the overall boat status.

Section I - General Regulations

A. Instructional language and commands

1. All orders, reports and feedback given while flooding, diving, surfacing, blowing etc. are to be repeated to guarantee they are understood correctly. The report of execution must follow every order.

2. When orders concerning the operation of shut off valves are given only the words "open" and "close" are to be used. In feedback about the position of the valve only the words "on" and "off" are to be used. Words such as "shut, tight and opened", are prohibited.
   Only standardized nomenclature (in accordance with the sketch book) is to be used in the naming of piping, shutoff valves etc.

...

B. Diving board, assignment board

11. Diving boards listing the steps which must be taken to prepare for diving are issued for every type of boat. The sailors who implement these measures or must take over responsibility for correct execution are listed on the assignment boards.

12. The measures concern:

I. Upper deck:
    a. seamanship,
    b. technical.
II Below deck:
  By compartment from aft to forward.

...

Section III - Readiness to dive

A. Commands

41. The Commander gives the order:

    Commander: "Prepare to dive",

    if necessary with restrictions (e.g. "except for diesels")

If circumstances require, it is first ordered:

     "Upper deck prepare to dive"

and later

    "Below deck prepare to dive".

42. This command is only given to the Engineering Officer. The Engineering Officer repeats it and passes it to all rooms verbally man to man.

B. Actions to be taken

43. Actions to be taken by the Watch Officer:

        a) prepare the upper deck to dive (Seamanship),

...

45. Explanation of 43:

In preparing the upper deck to dive the following directives are to be particularly emphasized:

No loose items may lie under the upper deck. All objects, such as lines, fenders, torpedo loading device, gangway, dingy, must be lashed, so that they cannot be knocked loose and foul the anchor or rescue equipment, air, diesel exhaust and vent ducting or also the propellers. The dogs of all access hatches and other fasteners must be checked for proper closing. Attention must be paid to the fact that the access hatches are closed correctly and do not rattle. The signal buoy (if installed) must be latched and secured. The drain and plug screw of the dingy must be open.

In readying the bridge, attention is to be paid to the fact that all folding seats are well secured because otherwise, they will rattle during submerged cruise. All wooden gratings need to be checked.

The speaking tube c**ks are closed on the order of the Commander. If they remain open at prepare to submerge, they must be closed not later than by the closing of the conning tower hatch.

...

47. The senior man in each room reports readiness to dive to the Engineering Officer.

...

C. Reports

51. The Commander receives the following reports by the Watch Officer (meaning the responsible Section Officer in each case):

        a) "Upper deck ready to dive",

         b) "Torpedo armament ready to dive",

        c) "Artillery ready to dive" and

        d) "Communications ready to dive".

...

56. The Commander is personally responsible for opening and closing the conning tower hatch. After opening or closing the Commander notifies the boat:

    Commander: "Conning tower hatch is open or closed".

After the ready to dive condition report has been issued there should be no interruptions. If however, an interruption is necessary, the Commander, the Engineering Officer and the Watch Officer must be informed simultaneously.

...

62. Condition of the boat:

    Boat is ready to dive, crew is at diving stations.

Orders and reports:

     Commander: "Closing conning tower hatch".

    Commander: "Conning tower hatch off. Negative pressure test".

The Order: "Coning tower hatch off" is passed to all rooms verbally man to man.