Holly did inform Artemis that the second lock will cause Armageddon.
Holly hugged her knees like a lost child. “The second releases Armageddon. If Opal succeeds in opening it, every single human on the surface of the earth will be killed.”
Eoin Colfer, “Artemis Fowl 08 - The Last Guardian”
Holly here told what she thought the lock would do. This story was told to her by her parents, neither of whom were around when the lock was created.
Bruin firstly explains it to Opal:
“Choose selflessly,” said Bruin’s voice from deep within the stone. “Prudence will close the gate entirely, releasing the souls and destroying the path forever. Desperation will summon the power of Danu and wipe the humans from the face of our land. Fairies shall walk the earth again.”
ibid
Opal explains to Artemis how the lock works.
“So here’s how it works,” said Opal brightly, as though explaining a math problem to her kindergarten group. “If I choose the first handprint, then I close the gate forever and all fairy souls inside the circle are released—except mine, of course, as I am protected by black magic. But if I choose the scary red hand, then the power of Danu is unleashed, but on humans only. It’s a pity we won’t see too much from here, but at least I can watch you die and imagine the magic’s effect on everyone else.”
ibid
And again this.
“Holly stopped struggling. “The magic shouldn’t affect a human, Artemis. Why hasn’t it released you yet?”
Artemis felt the magic scanning his person, looking for something. It found that something in his eye socket.
“I have a fairy eye—one of yours, remember?” said Artemis, pointing to the brown iris. “I thought my human genes could overcome that, but this is perceptive magic. Smart power.”
ibid