you really want to block off those holes then if you're not using egr. Think of it as restricting the airflow, putting in new hex bolts that are flat on the top (smooth so the air flows better) and without holes in them would create a less restrictive intake plenum, like an aftermarket intake, whereas stock with those egr discharge tubes would create restiction because they're right in the way of the airflow. It also makes sense to block off the holes since your not using egr also.
