Interesting thought. Are you talking about letting air in or out? Assuming out (pressure differential as rocket ascends), surprisingly I think they would reduce drag slightly if they were were behind the guide rail. The flow of air would essentially "fill the gap" of air (lower pressure zone) behind the lug. That would allow the air passing the lug to experience less turbulence and drag as it passes the back of the lug.
NASA and other private companies are currently experimenting with technologies using either blowing air from or applying suction to flying surfaces. This allows the point of transition of flow from laminar to turbulent, and hence the detachment point of the flow across the wing or fin, to happen much further along the chord. This is useful in either increasing the angle of attack limit, or reducing the drag on the aircraft (improving fuel efficiency). The same can be applied to the vertical tail so a small tail can still have the same control authority as a standard larger tail. That allows enough authority to keep the plane straight under asymmetric thrust conditions, but with a smaller tail surface area. The idea is to improve fuel economy by reducing the skin friction drag (less area) and by reducing vehicle mass.
So the short answer is probably, but almost immeasurably I think. If it makes sense aesthetically to remove holes and put them somewhere else then go for it. Don't do it just for less base drag. There would be insufficient mass flow out of the hole (in relation to the freestream velocity) of the rocket to make any significant effect I think.
On reading your post again I suspect you mean taking the air into the rocket. You are in effect trying to reduce the frontal area (sort of). If you could move it through without changing the total pressure (a measure of energy, sort of) it might work. Unfortunately moving air through hoses or compartments needs to be done exceptionally carefully to not lose that energy (in a jet engine for example it is very important for efficiency). So for what we are trying you would need a long skinny tube. If you try blowing down a long skinny tube you know that the back-pressure from the tube is significant. So that, in the rocket, would translate the total energy of the airflow into drag on the rocket before it got out the back end I think.
Total pressure (fluid dynamics concept) is really the pressure which is the sum of the static pressure in the area, plus the dynamic pressure, plus the pressure head due to height difference of the ends.