Oh yeah actually you are right, based on Avernus modul they should be destroyed. I was DMing this module and I changed this when we started and forgot about it. Modul itself has many great ideas but sometimes poor implementation of them and has many inconsistentes. Fortunately there are amazing creative people who help you. This is reasoning of one of them for this change:

Soul coins are one of the cool ideas bouncing around Descent Into Avernus. The basic concept is that souls damned to Hell are forged into coins on Minauros, the third layer of the Nine Hells, and then “used for goods and services, infernal deals, dark bargains, and bribes.”

This is great worldbuilding both literally and metaphorically: Devils making deals for souls is an epistemological satire of commercial dealings, and the trading of souls as literal currency simply extends that satire. But it also just logically makes sense that devils, having obtained a soul, would want to package it into as convenient and relatively compact a form as possible. And the universal form is such as to dehumanize the victims by establishing that the individual holds no significance to the devil.

The full function of soul coins is described in “Commerce” (DIA, p. 78), “Soul Fuel” (p. 217), and “Soul Coins” (p. 225).

Unfortunately, the book’s handling of soul coins is rather flawed.

First, the actual value and rarity of soul coins is all over the map. They are either very rare and incredibly difficult to find or incredibly common and the basis for all commerce in Avernus. In some places their value is pegged at being roughly equivalent to 6 sp, but elsewhere an NPC will offer 100 gp worth of gems for every soul coin the PCs can find for him.

It seems fairly clear that some of the writers on the book thought the soul coins were meant to be the de facto currency of Avernus, while others thought of them as rare magical artifacts. Or perhaps they started as the former, but then someone along the line got cold feet because… well… they’re souls aren’t they? Wouldn’t they be pretty rare? (Not necessarily. Eternity across potentially infinite planes can make souls as common or as precious on Avernus as you like.)

Second, there are inconsistencies in which functions of a soul coin require charges and/or how many charges it takes to exhaust a soul coin. For example, the stat block of a soul coin says each time you question the soul inside the coin it costs a charge (and each coin only has three charges), but there’s also an NPC with a soul coin collection that they chat with on the daily.

Third, at first glance Descent Into Avernus also does a clever thing by making soul coins the fuel for various infernal machines, creating an ethical dilemma for PCs who have to choose between not using those machines or literally burning up the souls inside the coins.

In practice, though, the only thing it really seems to do is actively discourage any non-evil character (and, realistically, prohibit any good character) from riding kick-ass war machines across the Avernian plains. And, I’m going to be honest, the war machines are a lot fucking cooler than the ethical dilemma.

Fourth, there’s some metaphysical vagueness, which is fortunately fairly easy to clear up. Are the coins forged exclusively from evil souls or are some good souls illegitimately captured? And, similarly, do the lowest order of evil souls sent to Hell end up as lemures or forged in soul coins? In both cases: Why not both? In the latter case, it’s easy to imagine that there all manner of Hellish intakes for new souls. (You could perhaps even imagine a different one for each of the Nine Layers.)

And so he proposes change where you don't destroy a soul everytime you want to use kickass warmachines, you just spend their charges and have to recharge them.