Still looking into the how I did this. I'll add this bit of info though, the game considers you either surfaced or submerged with no in between. Once flagged as submerged the radio is disabled along with the diesel engines, unless you have a snorkel equipped. New options become available once submerged as well like emergency surface, deploying decoys, and silent running. There is another controller for when the deck crew moves below decks that doesn't coincide with the surfaced/submerged flag. Using my Skipjack as an example, you can be "submerged" at 32ft with the bridge still manned until 35ft!
Thus far I've tried changing settings in the sim and cfg files to no effect. I want to say it's either 3d model based or node location based, which one of either one is anybodies guess at this point. I'm going to try to recreate one of the nuc subs this weekend and perform more rigorous testing to see if I can uncover an answer.