"The flow inside the hole (which would be like flow inside a pipe) would create a massive skin friction drag and a turbulent flow inside the pipe. Flow inside pipes typically have a high drag.
This flow would pass out the back of the bomb into a region which (with no hole) would have been undisturbed and so this would maybe create a tubulent region behind the bomb, increasing the pressure drag."
I think you overestimate the effect of skin friction vs. pressure drag, but I will grant you I may be thinking at a Re much larger than you are which may affect things. I.e., your arguement might hold at low Reynold's numbers. At anything over Re = 10k or so:
Take the viewpoint of an air molecule, approaching along the centerline of the bomb. The closed bomb forced that air molecule to diverge around the maximum diameter of the bomb, and all the adjacent air molecules move too. At the back of the bomb, there is a turbulent wake, and a seperated, low-pressure region.
Take the second case, same setup, the air molecule blows thru the center of the casing, retarded somewhat by adjacent molecules via skin friction to the "pipe". But the pressure drag, by far the larger effect, is greatly reduced by the air flow into the base region from the hole. Any skin friction in the "pipe" can only be generated by a pressure differential from front-to-back on the body, and so cannot be high enough, or remove more energy from the flow, than the body is capable of generating in the first place.
Take the thought experiment to the extreme - a 4" diameter bar, vs. a 4" pipe with 1/8" wall. Which has the lower drag?
Any flow thru the hole will reduce the overall body drag, since less air is required to be disturbed by the body's passage than if the hole was not there.