What is the difference between Has he come? and Did he come?
Is the headline of the linked article correct?
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This is simply the question form of sentence that use the perfect tense:
He went to Morocco.
Did he go to Morocco?
He has been to Morocco
Has he been to Morocco?
In the same way:
(This) aircraft has covered (those) aircraft.
Has (this) aircraft covered (those) aircraft?
The present perfect form indicates "life experience", although in this case it's not referring to any specific person's life but rather the general existence of some experience/event. The meaning is to suggest some experience did happen.
As you expect, it would have been more straightforward to simply ask, "Did aircraft A cover aircraft B & C?" but "has" still gets the meaning across.
Side note: Here "covered" means "to provide support in the form of 'radar coverage'", although in this case it seems perhaps the "spy" aircraft were used to deter the Russians from using their own radar to track the stealth fighters? Something like that. The language is full of military jargon and is slightly confusing.