If your opponent is human: ....if your opponent is human (and good), odds are you won't want to stack your modern navy (on defense). you mentioned destroyers, battleships and subs. A good human opponent will amphibiously invade your cities if you "hide" your ships in there and wipe them out without a fight....other good human opponents will tac nuke your stacks.
so, if you actually have a fairly big kickass circa 1940's navy, versus human, I recommend actually what bombardment attempted to make players do...spread your navy out. and subs, lots of subs. cheaper, and forces the human player to find them to wipe them out. Also, it would be a hassle for the human player to knock them out one by one to drive toward your coast. Also, subs are good scouts for you. oh, and another thing...if it turns out all is lost, and you are looking at ending up in tundra hell as a pseudo vassal....subs can hide under ocean ice.....at least it's a spite for the AI who tried to get you...and maybe those 5 or 6 subs you can save that way can get their vengeance next war....
If the enemy is AI....the enemy has gotten much better at amphibious assaults, but if your coastal cities are garrisonned with confidence, on defense, I'm a big fan of building either a fort near a hidden lake and sequestering in the lake, or hiding in the city. Nothing beats having your subs and destroyers dart out, survive an attack, and come back to the city disallowing the AI to counterattack via convential naval warfare. Of course, you haven't mentioned nukes. the only real defense against nukes is SDI in this game. (again, spreading your units out is another semi-feasible defense.
I'm a big fan of gracchus' comment about carriers. Carriers and air support on a stack is CRUCIAL in naval combat....but since you did say defense, it is possible to base your fighters in a nearby city or fort and run air defense missions on assets fairly close to your coast. But if you lack air power, well, your original post said only subs, destroyers and Battlewagons....if that's all I had to work with and all I wanted was a defensive stance (and didn't have nukes) I'd want a ratio of 50% subs (all with tactics, maybe a few scouts with sentry), 30% destroyers, 20% battlewagons. if you are on defense, your defense objective is to SINK invading transports, or make that assault task force PAY for succeffully dropping troops on a beachhead. You will expect to lose a lot of your defensive navy. The battlewagons would be promoted up the barrage promo ladder, the destroyers maybe up the combat ladder (or tactics/withdraw), subs definitely up the withdraw/tactics as mentioned....enemy stack comes, your battlecans will go down to their combat promoted ones, but your BB screen acts just like suicide catapults....from experience as to what cats do on land, if your destroyers are now in the 80% pick-off rate, damn the torpedoes full speed ahead with your tin cans.....if still not there, then let 'em have it with the subs....knowing how the AI deals with me, a two-promoted withdraw sub (30% withdraw chance?) typically withdraws a LOT and do nasty damage (most likely returning to a safe city or fort)....then let 'em have it with the tin cans.
from my experience, if you are on defense, and your power rating didn't dissuade the AI from calling off a planned war, the AI WILL declare, and surprise drop....not much you can do about it (except on earth maps in the pacific, your subs SHOULD see china or japan coming at least 1 turn before with their death stack...odds are your death stack couldn't reach them to STOP them from landing, but you could position for that next turn and then declare on THEM...)
so you most likely will have to deal with a land war....but it is the job of your rear admiral in command of Defense task forces to make sure, by God, their victory was a phyrric one....