Well, I wouldn't say that SS killed the game, but they did certainly CHANGED the game... or better said, they SHOULD change the player mindset.
For starters, traditional BB crew setups should change. Old-school 6/4 (engineers/repairers) setups are now outdated, and at least one space has to be allocated to an (P)HH gunner (one is more than enough from my experience); in my case, a repairer is gone.
If AA gunners are already in place their function now has to be two-folded or entirely different. If your ship has "enough" T slots you could use some of them for AA guns and others for (P)HH guns, using different binds for different shells; i.e., Bind A for AA shells, Bind B for (P)HH shells so as not to mess your shots; SS incoming, press Y (plus F4 for gradual), SS gone, press Y again (plus F4 for max) so you keep on taking planes down. If your ship does not have "enough" T slots then you should consider entirely changing your AA gunners' role to permanent ASWers with (P)HH guns.
Naturally it is far more difficult to defend your BB from SS attacks if you can't actually see them. To depend on FFs, DDs, SSs, or other ships with sonar is not a safe bet since there could be none around or their sonar could deactivate at crucial times due to OH. Therefore, another mindset has to be changed and that is the use of an escort with an active sonar, either built-in or with sonarman on board. Not too many people are fond of the use of an escort but it could be your lifesaver. Besides more burden will be on your shoulders since you have to be aware of your escort position in the heat of the battle to avoid it from being taken down by either friendly or enemy fire but it is worth since that sonar capability can help you land much more precise (P)HH shots to take down those pesky subs. You could use a cheap FF if you dont want to be too focused on preserving it or you could use an Emden with AA + sonarman.
As for CVs something around the lines of BBs as expressed above is the change they should adapt to. To preserve a valuable support slot, a sonarman should be on an escort and since CVs are usually at the back they shouldn't worry much about where their escorts are wandering around.
In the end, I do not fear subs; i actually really hope they come south where I always go as I really do enjoy sinking them! (provided my escort is still alive :)
===> I do fear to enter a room and then CRASH when almost ready to start, or when at the battle ready logo, or when the battle actually begins, or whenever it wants to crash! I do fear to get LAGGED midgame and have my guns jump all over the place, or get my screen frozen for 15 seconds only to find I'm in the middle of nowhere shells flying towards me, or to suddenly get the infamous DISCONNECT message. Man do i fear to realize I'm in a DESYNC'd room and suddenly everyone crashes but me and a lone enemy CV in the far opposite corner of the map.
==============> Those 4 LCDD NF devils are the REAL game KILLERS: Lag, Crash, Desync, Disconnect! SSs are just a small blemish in comparison.