The only realistic reason to mod additional internal slots is to have space to reload the initially loaded torpedos, as long as you didn't have fired one.
I used to have only three tubes loaded to simulate the electrics to be maintained. I did even simulate the change of pistols by reloading the tubes accordingly.
Well, I did it to ramp up realism, but today I prefer to let my crew manage it for me.
I didn't find a way to have an empty slot while operating the loadout screen in base. I simply shot two eels into the harbour walls at the beginning of my sortie to have a forward and a backward empty internal slot.
If you want to do so, modify Basic.cfg, add two new slots:
[SUBMARINE_AMMO2]; VIIB
Type=1
Version=0
ForeTubes=4
AftTubes=1
ForeResIntern=4
ForeResExtern=1
ForeResExtra=2
<-3
AftResIntern=1
<-2
AftResExtern=1
ShellSlots=12
NbYears=7
Renown=3
SNK_MASK=NSS_Uboattype7_SNK_mask
Now define the loadout for those new slots, they show up in the loadout screen:
Year0=1939
ForeTube00=0 ;T1
ForeTube01=0
ForeTube02=0
ForeTube03=2
ForeResIntern00=2
ForeResIntern01=2
ForeResIntern02=0
ForeResIntern03=0
ForeResExtern00=0
ForeResExtra00=0
ForeResExtra01=0
ForeResExtra02=0
AftTubes00=0
AftResIntern00=2
AftResIntern01=2
AftResExtern00=0
Z01_00=3 ; VIIB/1
M01_00=1
A01_00=8
SuperCharger_00=1260; GWX V2.1: was -1, so this boat now has GW turbos by default
Snorkel_00=-1
Batteries_00=1265
AftBatteries_00=1265
Hydrophone_00=1270
Sonar_00=-1
Radar_00=-1
RadarWarningReceiver_00=-1
Decoy_Launcher_00=-1
SonarCoatings_00=-1
RadarCoatings_00=-1
Renown0=2500
The lines read [x for year][y for tube]=[z for torpedo type]
The first position (x) indicates the year starting with 0 for 1939 and adds up for every next year ( 1942 would be the fourth year of war indicated by '3') - change the lines in the corresponding blocks for your type of U-Boot.
The second position (y) indicates the tube/slot - again starting with 0 for tube/slot 1 ( '5' would indicate tube/slot 6)
The third position (z) indicates the type of torpedo to be loaded in the base's loadout screen.
0 = G7a/T1
1 = G7aFAT
2 = G7e/T2 first version
3 = G7e/T3 second version
4 = ??? - not sure right now - G7eFAT iirc
5 = Falke
6 =
well the rest is lost somewhere in the endless emptiness of my brain...