Yes cap it, seal it, if you are not going to use it.
Pull the cap or hose or vacuum gauge, whatever the case may be, off that nipple with the engine idling and you'll immediately see why you can't have it sucking in all that air.
BTW, the hose on that nipple is not supposed to go to the CC..It's supposed to go to the ARV...to that nipple shown in the link I provided that is labeled "VACUUM"