There is no reason to use the past perfect, as it does not alter the meaning of the sentence in any way. The speaker could have said:
... even the earliest human beings asked themselves the questions ...
I expect the most common reason you hear this in unscripted narrative is that the speaker has a particular time frame in mind and is unconsciously relating one event to some subsequent event, possibly (as Tᴚoɯɐuo says) the speaker's own current speculation.
There is nothing ungrammatical about this use of the past perfect here. All it means is that the expected reference to another event has been left out as unimportant. This also gives some insight into the speaker's frame of mind -- but this too might not be especially significant.
When speculating about the construction of the Pyramids, many believed that the Egyptians had built them using slave labor, but archaeologists have evidence that the builders were ordinary laborers more akin to feudal serfs than what we think of as "slaves".
Again, no reason to use the past perfect, except that the writer unconsciously relates the time frame of the building to the time frame of the speculating,