leave them in or take them out it ain't going to make a major difference unless you were to start mearsuing the the air flow, logic says that with them wide open but still in place you would need to have slightly slower airflow due to the air being slowed over the surface of the plates but I doubt if you would feel it with a butt dyno, so if you want max air flow rip them out if you are planning on draging every last bit of air flow but then even the shafts left behind are going to cause some distrubance in the air, I have mine out but it depends on if
you want to really