That is the coolant port. There should be two on the throttle body. It warms the throttle body to get better emmissions. Most people disconnect them and just loop one of the hoses between the two coolant pipes on the intake.
You can cap them, you can leave them open. You can cap one and leave the other open. Doesn't really matter. I've always just left them open. Some people cap them probably so that it doesn't look like something is missing. I have heard of people having trouble with smog testing because the tech thinks it is a vacuum line unplugged.