As it says in the post, in most missions, you can just ignore enemy submarines entirely, even those missions with a focus on them, at least in the current update.
I thought I was going crazy trying to make my own mission with submarines, and they would not do what they were told to do, so I loaded up the third mission of Molniya campaign to see what they did differently. Turns out, the subs are just a broken there too.
Using debug mode, Sculpin spawned at the X point, as intended, and proceeded to do circles for 3 hours, stuck in "Building Solution to Track"
S99 did the same thing, spun in circles for 3 hours in "Building Solution to Track"
S97 actually did something, except instead it steamed directly to the merchants and torpedoed Dnestr.
In all three cases, the submarines completely ignore any waypoints, depths, speeds, and attack points given to them in the mission editor, when in control of the enemy AI, which makes it frustratingly hard to make any missions including enemy submarines, because they are an empty threat.
The submarines acting like this completely break the mission itself, as Amperter is supposed to be sunk early on after the periscope reveal if you dont do anything, which in itself would cause the American SSN search area to not appear, as intended. But due to the subs just doing nothing, nothing happens, you can just x100 the mission for hours on end.
Additionally, even if you give the enemy AI perfect detects on the units you want them to attack, using the Reveal Units function, it still gets stuck in building solution to track.