I think you are right that evolution is not fussy about whether the punished agent understands the causality just so long as there is causation both from genes to crimes and from genes to punishment. That second causation (genes to punishment) may be through the causal intermediary of the crime, though it doesn't have to be.

Evolution is a kind of learning, but it isn't the organism that learns - it is the species. And, of course, evolution can learn even if punishment falls on the offspring [Edit: was "can direct the punishment to offspring"], rather than the actual offender. Deuteronomy 5:9 is much closer to Darwin than is Genesis.

If you want to have organisms do the learning, though, you need to direct the punishment more carefully, and to make the causal link between crime and punishment more obvious to the organism. We can distinguish two kinds of learning - unconscious (for example, operant conditioning) and conscious (game theory and rational agents).

As you point out, you can get learning from punishment, even if the organism is not aware of the causality - but it does seem that the punishment must be close in time to the action which provokes the punishment. Unconscious learning cannot work otherwise.

But with conscious learning, the punishment need not be close in time to the 'crime' - consciousness and language permit the linkage to be signaled by other cues. But I'm pretty sure it is important that it be noticed by the punished agent that the punishment is flowing from another conscious agent, that the reason for receiving punishment has to do with failure to adhere to an implicit or explicit bargain which exists between punisher and punishee, and that to avoid additional punishment it is necessary to get into conformance with the bargain.