Some racers like to glue the inner side wall to the wheel for added support and the holes allow for this; venting the tires is still needed regardless of the holes. We really haven't seen or heard any concerns regarding the holes until your post. There are no plans to change the mold to cover the holes.
I mentioned to Jason at the Alabama race that the new wheels made it alot easier to get water in the tire when washing. Esepcially when cleaning any mud or loam out of the inside of the wheels.