As other have mentioned, this is a very old argument. From a game-play standpoint, the infinite torpedo's really don't exist. Combat lasts at best for a few minutes, before you have a chance to cool-down and reload. So while in practice they have not replenishment requirements, in reality it's balanced for game play.
I agree with your comment in principle - especially now that the new torpedoes from reputation have 'magazines' - that it would be nice that all torpedo's have stocking limits. Reality says though that Cryptic cannot make such a fundamental change without serious damage to playability.
One option could be the addition of 'expendable' torpedo warheads as ship devices. Each use would upgrade your next torpedo shot. This would enable starship's to have a variable weapons load-out option beyond the established torpedo types. The onus would be on Captains to have these in inventory and 'pull them out' as needed. We all remember Janeway pulling a tricobalt warhead when needed, from a limited arsenal.
These warheads could be built through doff assignments, or purchased for dilithium through your local Starbase. They would not be as effective as your principle launcher, and not all types or warheads would necessarily work with your launcher due to the technical limitations.
Mission-specific warheads could be part of the experience.
At any rate this would provide some flexibility to warhead and yield capability while giving the players a more realistic torpedo experience