I refuse to believe that the designers of the hatches made a question mark in the ground; Eko even said it was a circle, not a question mark. I think it was definitely a circle, which they (Dharma, or whoever) made by salting the earth there, and the hatch door was below it, and it only looked like a question mark because the plane was burnt, and it caused a darkening of the area below the circle. So it kind of looked like a question mark, probably on purpose by the writers so we'd discuss it to no end, but I don't believe it was designed that way by Dharma.