I noticed this too, mine has 2 very large holes, has the design changed since i bought mine years ago?
The Akasa Eclipse Case changed the removable motherboard tray layout from two vent holes to one about 6 months ago, all Akasa's are now shipping with one vent hole on the motherboard tray, unless you get sent cases from old stock. I must admit I do prefer the tray with the two vents as cabling is easier to manage.