Nope, the holes are in the intake manifold where the EGR valve (you are calling "vacuum actuator") is mounted.
One of them connects to the exhaust side, and the other connects to the intake manifold side, and the vacuum actuator allows exhaust gasses to go from one hole to the other. Correct?
You can either leave the EGR valve in place and just not hook it to anything, in which case it will never open, or if you want a cleaner underhood appearance, replace the valve with a blockoff plate p/n 3671 447 from the dealer. Use a new EGR valve gasket to seal it.
