My experience with depth charges close enough to kill crew members is that they usually wreck the sub anyway, so I never bothered looking for a way to protect the deck crew. One obvious option would be to select crewman with high numbers in mechanics, guns, and watch, put them on deck when surfaced and move them into the forward torpedo room and damage control when submerged. If you stop and think about it whenever you're reloading the tubes or repairing damage you're usually submerged anyway, so you don't need deck watch.
Other item that might be worth experimenting - \Data\UPCData\UPCUnitsData\UnitParts(subtype).upc seems to focus on the deck crew;
[UnitPart 1.Compartment 1]
CompartmentType= 1
StatusActive= Yes
ID= PorpoiseConnWatch
NameDisplayable= Deck Watch
Type=NULL
FunctionalType= ObservationRoom
MechanicalCoef= 0.2 ;0..1
ElectricsCoef= 0.2 ;0..1
GunsCoef= 0.2 ;0..1
WatchmanCoef= 1.0 ;0..1
WatchStandingCoef= 0.048
MaintenanceCoef= 0.0144
RepairsCoef= 0.072
ReloadingweaponCoef= 0.072
SleepCoef= -0.12
LeadersSlots=3
CrewMembersSlots= 9
EffciencyDenominator=4
EffciencyDenominatorBS=8
Hitpoints=200
CrewExposure=0.3
EquipmentsExposure=0.1
WeaponsExposure=0.1
ExternalDamageZoneTypeID3D= 31
DamageDescription1= NULL, 0, 0.2, 0, 1, 1, Minor damage, 0, 0, NULL, 0, 0.2, 0.2
DamageDescription2= NULL, 0.2, 0.6, 0, 1, 1, Medium damage, 0, 0, NULL, 0, 0.2, 0.5
DamageDescription3= NULL, 0.6, 1, 0, 1, 1, Heavy damage, 0, 0, NULL, 0, 0.2, 1
[UnitPart 1.Compartment 2]
CompartmentType= 2
StatusActive= No
ID= PorpoiseConnAA
NameDisplayable= AA Gun
Type=NULL
FunctionalType= FlakRoom
MechanicalCoef= 0.2
ElectricsCoef= 0
GunsCoef= 0.5 ;0..1
WatchmanCoef= 0.5
WatchStandingCoef= 0.048
MaintenanceCoef= 0.0144
RepairsCoef= 0.072
ReloadingweaponCoef= 0.072
SleepCoef= -0.12
LeadersSlots=0
CrewMembersSlots= 0
EffciencyDenominator=1
EffciencyDenominatorBS=1
Hitpoints=200
CrewExposure=0.3
EquipmentsExposure=0.1
WeaponsExposure=0.1
ExternalDamageZoneTypeID3D= 44
DamageDescription1= NULL, 0, 0.2, 0, 1, 1, Minor damage, 0, 0, NULL, 0, 0.2, 0.2
DamageDescription2= NULL, 0.2, 0.6, 0, 1, 1, Medium damage, 0, 0, NULL, 0, 0.2, 0.5
DamageDescription3= NULL, 0.6, 1, 0, 1, 1, Heavy damage, 0, 0, NULL, 0, 0.2, 1
;------------------------------------------------------------
; CREWMEMBER SLOTS
;
;
;Type= Officer ;for Officers slots, which should be located in the Command Room and give bonus to the entire unit
;Type= Leader ;for Leaders slots, which give bonus to the compartment
;Type= Crewman ;for crewmember slots, which work and get poor pay
;
Changing crew exposure to something like 0.01 MIGHT reduce how much exposure they have to getting wounded. I say "MIGHT" because I haven't tried it, and you have to keep in mind that SH4 is really SH3 with heavy modifications, and the ubisoft programmers didn't bother deleting half of the u-boat files and/or programming from SH3 which are not actually used.
Example;
[Unit]
ClassName=SSGato
3DModelFileName=data/Submarine/NSS_Gato/NSS_Gato
HumanPlayable=YES
Interior=data/Interior/NSS_Gato/NSS_Gato
UnitType=200
MaxSpeed=21
MaxSpeedSubmerged=9
Length=95
Width=8.3
RenownAwarded=130
You would THINK that it's possible to change the max speed of the sub in that file, but it actually does nothing since the performance data used is in the NSS_Gato.sim file. SOME of the data in the (subtype).cfg file IS used, but other parts are ignored. Only way to find out is experiment with it.