I agree with Jay and Gary Botnovcan's answers regarding the grammar differences between "has" and "had," but more to the point, here is why I do not think the suggestion of changing "Putin has" to "Putin had" is a good one in this case: because it makes a fairly substantive change in meaning.
The use of "has cut off" as opposed to just "cut off" and especially in contrast with "had cut off" implies that the action happened relatively recently. Indeed, if we read the article, that is the case.
The article states that mercantile vessels and some other vessels should have access to Ukraine's port as per an agreement that took place in 2003. But Putin only closed the straight leading to the port two weeks ago.
The action of Putin cutting off the ports happened in the past, sure – so Trump has had time to notice – but it's not that far in the past, and that is the real point here.
Russia's aggression in the Ukraine is a slow-moving event. Putin isn't launching a full-scale invasion of Ukraine; instead, he's making baby steps toward having more and more control over Ukraine over a number of years. (The article mentions that it's been three years since Russia annexed Crimea.) So the headline is basically saying "has Trump noticed that Russia is taking yet another step toward taking over Ukraine as we speak?"
As Jay mentions, the use of "has cut off" indicates the ports are still cut off, but it also indicates that the period where other governments could respond to what they perceive as a political threat by Russia is also still happening – we're not so far past the ports being cut off that everybody is just accepting that they did it. It's still a relatively new event, and there's still an opening for other governments to speak up about it.
Another reason I don't think we can change "Putin has" to "Putin had" here without making any additional changes to the headline is because it wouldn't make sense in contrast with "has Trump noticed." If Putin had cut off the ports in the past, the verb for Trump noticing would have to change.
You don't notice something that already happened. You notice it when it's happening, or else you find out about it later. So if the verb is "had," the headline would have to say something like:
- Did Trump notice that Putin had cut off Ukraine’s Black Sea Ports? or
– Was Trump aware that Putin had cut off Ukraine's Black Sea Ports?
But those headlines don't make sense at the moment because the ports just closed. They might make sense in some future article about what happened after Putin closed the ports.