How are they not rational? Violence is a tool. They operate an illegal business so they can’t sue other parties for breach of contract. They can't call the police if they are robbed or file an insurance claim for what was taken. Even the over-the-top violence has a rationale. They aren't punishing the victims as much as they are attempting to broadcast that there is a higher price to be paid than any gain from giving information, to reduce their future losses and enforcement efforts. It isn’t moral or ethical, but I wouldn’t say it is irrational.
> How are they not rational?
It's the meth.
Lots of organized crime around the world manages to operate without cutting all the limbs off somebody then arranging them like flowers in a "vase" made out of the poor soul's ribcage. The cartels take violence far beyond what is pragmatically necessary. Their system of crime breeds excessive violence and insanity.