No matter what the location, height, or depth, the Twilight Crystals could appear anywhere: at the bottom of the ocean, on a floating island, or right in a wall, which was the most common occurrence.
The Kirani Bugs knew where all their Twilight Crystals were located, and these were not the most easily accessible places, so they were confident that this would help them buy time.
However, Adam's desire to know the limits of his abilities ruined their plans.
If he had used a vertical cut, he would most likely have exposed the Twilight Crystal, because he would have had to hit it directly. The chances of that were quite slim.
Because he cut the wall in half horizontally, he exposed everything behind it.
There should have been a stone or other tunnels, of which there were dozens at the Kirani Colony, but what he found turned out to be the most valuable thing possible.
