“He could have done it.” ( crime )

A detective is reviewing his list of suspects in an art heist. The theft from a wealthy home seems to be an inside job. John is a nephew of the owner and was staying at the house. The detective concludes: “John could have done it. He had the ability and the opportunity. But, although he might be our thief, I would put three other people in front of him as more likely suspects.”

In effect, the detective concedes “could have, but probably didn’t.” And since we don’t know whether he did or didn’t, there is no connection to any counterfactual suppositions about what John would have done if…. “Could have” in this usage is particularly detached from the counterfactual “would have if…”.

Notice how “could have” focuses on ability and opportunity while leaving other “springs” of action open. The detective could say “He could have done it, but I don’t see a compelling motive”, or “He could have done it, but it would be completely inconsistent with his character” . But the detective could not say “He could have done it but he had no opportunity to do it” or “He could have done it but he was not physically able to do it.”

“He could have done it “ascribes ability to an agent at a past time. Notice that it is the context and background information that determine whether there is an implication that he did not do what we suppose he was able to do. Grammar does not require that “could have” be uttered in reference to something that didn’t happen. “Could have done x ” is not necessarily, or even usually, the apodosis verb in a counterfactual conditional with a suppressed protasis.
“Could have” works fine ascribing an ability in a context like this where there is no counterfactual supposition in play about the use of that ability.