FUBAR295 listed my mod, which, AFAIK, is the only one that simulates it. However, I would like to point out that it does so poorly, as there is no mechanism in game to "stop and board."
Basically, there was a procedure for stopping and boarding in the
U-Boat Commander's Handbook. Although the book was produced in late 1942, the "stop and board" procedure was in effect from the early days of the war. In summary, it said that you should inspect the ship via periscope. Then wait until the ship passes and gets to a range greater than 4km. Then surface and approach the ship at high speed.
IRL, the surface ship captain would have to make a decision, submit to being searched for contraband or try to outrun the surfaced sub. If they submit, then the uboat boards and looks for contraband,
e.g. cargo that is destined for an enemy port. If none is found, the ship is allowed to continue on its way. If contraband is found, the ship was allowed to be taken in prize if a prize crew could be formed. If not, then it could be sunk. Very quickly, sinking the ship became the norm, as reducing your uboat crew would hamper operational readiness. Then the prize rules were abrogated as the war went on.
As a side note, if it started shooting at the sub at all, it was, of course, eligible to be sunk.
However, in SH3, once you surface and charge the ship, if it is enemy, it inevitably tries to run by slowing down
and weaving.
So I do the inspection, let it get out to 4km, surface, and charge the ship. If it doesn't weave, I pull up close to it and eventually continue on my way. If it weaves, I sink it, requiring myself to hit it with one torpedo if its tonnage is greater than 3kt before I use my deck gun. This is a "realism" decision based on my research for the mod.
Outside of that, I don't know if anything else simulates it.