Dark Waters is based upon Operation Monsun, and has the same issue with turm upgrades, in that they usually (not always) fail. In SH4, all items connected with the sub and turm have to match for an upgrade to succeed. Also, quite a few of the submarines in OM (DW) came from SH3, where the "upgrade" process is initiated by the player. In SH4, the "game" does it 'automatically', based upon Renown score, and the players patrol and career ranking system - which I think has "bad math" in its equations, but that is my opinion and is not based on anything "scientific". I have played the Stock game on the German side before, and even in it, with only the Type IX to worry about, the devs seem to have failed in their implementation. KSD may have "fixed" - but I do not remember... sorry.
