Compared to the availability of bombs, the availability of torpedoes is intended to be restricted in AE. You are all overlooking the tools on hand for the devs to achieve this relative scarcity without having to undertake a very serious code rewrite.
1. Air launched torpedoes came under the purview of the Air Team. Sea launched torpedoes came under the purview of the Naval Team. Just as the disbanding rules were implemented differently by the Land Team compared to how the Air Team handled it (and the close cousin, ship withdrawal by the Naval Team), you have two different solutions.
2. The Naval Team independently developed a much more rigorous structure for rearming vessels. Port size, ship tenders, naval support squads, operational points et al, could be used to restrict the rearming of sea launched torpedoes. Even the possibility of damage to the torpedo weapon slots and the consequent issue of getting them "repaired", adds further tools to the Naval Team.
3. By contrast to the tools available to the Naval Team, the Air Team had virtually none. Rearming any type of aircraft at an airfield is extremely abstracted. There is a different cost in supply consumption between rearming a 16" naval gun and a 40mm Bofors. Now compare that naval rearming cost with the supply consumption cost of rearming an aircraft. Try spotting the supply cost differential between rearming a fighter aircraft with .303 bullets, or a Wirraway with it's 100lb bombs, or the 500lb bombs of a Liberator. Don't forget that size of airfield, unlike port size, doesn't come into play.
4. Considering their available tools, the Air Team decided to separate air launched torpedo rearming from the bog standard aircraft rearming approach. A simplistic supply quantum presence, scaled to airfield size (but note this has nothing to do with actual supply consumption ) together with the airfield falling within the umbrella of Air HQ/Command HQ range, would be necessary for the availability of air launched torpedoes at that airfield. There aren't that many Air/Command HQs so that acts to achieve relative scarcity. To enable Base Forces to also dispense torpedoes was considered by the devs to seriously unbalance the game as it really would provide no limit on the availability of air launched torpedoes. Just count up the number of Base Forces in the game compared with the number of Air/Command HQs.
5. It was not the responsibility of the Air Team to fiddle with Naval HQs, which was not in their purview, in order to accommodate air launched torpedoes. As far as the Naval Team was concerned, there was no need for them to fiddle with Naval HQs (which was in their purview) to accommodate sea launched torpedoes as that issue was more than adequately covered by their much more robust existing logistics system.
6. There was dev consideration given to making torpedoes a buildable device, like mines are. but there were too many problems with the idea.
(a) Mines, which are deployed in minefields, are quasi tracked. There is no similar tracking of torpedoes.
(b) Mine production rates are low and this is tolerable because the game has ACMs to maintain minefields, again nothing comparable exists for torpedoes. Besides it was a widespread complaint of classical WITP that mining was overpowered. Can you imagine the all mighty roar of criticism if the historical torpedo production rates were applied in AE.
(c) Then again mines don't have varying dud rates whereas Allied torpedoes do. Try balancing that when limited torpedo production is introduced into the matrix.
Once again, repeat after me, AE is full of abstractions. Trying to quibble with how the devs decided to abstract "x" in order that it fitted with the code, is the road to madness.