I'm not missing anything at all.
I'm challenging why there is a belief that everything has to be equal and balanced. And why, if everything is balanced, it has to be equal to the lowest cost.
There is absolutely nothing that says all assets should be used. It's a fallacy based on the artifice that everything should be equitable.
In this specific instance you have two weapons with very different outcomes and effectiveness and with different costs.
Changing the synth costs of shock cannon reloads does not buff their performance - it makes them a viable option for sustained use.
This is demonstrably nonsense. Having more ammunition available for less cost clearly improves your ability to engage in combat. You clearly favour Frags in combat (they are the "obvious choice in nearly every single encounter") ostensibly because of the cost of the ammunition. You cannot claim that one weapon is preferable over another due to its ammunition cost and then claim in the same paragraph that the ammunition cost isn't a factor.