The deck gun is only there to tacke small ships that don't warrent a torpedo or to finnish off a larger vessel that you had already damaged with torpedoes and was taking its time sinking.
TM uses a damage model called Natural Sinking Mechanics. This model sinks vessels through flooding, pretty much exclusively, rather than by simply ticking off enough damage points for the ship to sink. This simultes the sinking mechanics that a RL ship would have. A 6000 ton frieghter would easily soak up twice the number of AP shells in RL, unless you hit it under the water line to induce flooding to begin and then it would take a very long time to flood becuse the holes punched by a 4 or 3 inch shell would not be very big.
AP shells are best left for tackling small warships that have some degree of armour plating, they would simply go strait through a merchant without exploding (the game models this). HE is better for merchants it does more damage.
Try to hit more below the water line and the deck gun will be more effective at sinking ships.
As to the AA guns, are you using the 50 cal as an AA gun? If so it has poor elevation so unless the aircraft was coming in low (and they never do this in SH4) the AI gunner would not be able to fire. Select a 20mm cannon next time you finnish a patrol. Otherwise, make sure you have a crew member assigned to the AA gun slot on the crew manager screen.
Probably the best strategy when faced with an enemy aircraft is to crash dive imediately rather than fight it out on the surace (unless you can't dive for some reason eg. damage). A direct bomb hit on your sub can really ruin your day!
TM also remapped the keys try using you mouse wheel to access the binoculars.