The openings behind the cowl were most likely cooling holes designed to reduce temperatures behind the engine and every wartime photo of a Ki-84 I have shows them on both sides of the fuselage. The only aircraft that I have seen that has the holes covered is in a museum, my guess is the covers were added by museum staff who assumed they had been previously looted off the aircraft.
I painted the holes in black on the diffuse map and on the topmost layer, above all the weathering etc. They are black on the specular, power and environment maps too, so the holes reflect no light at all. On the normal map they are a darker grey than the surrounding metal to get a sunken effect, so for instance with sunlight shining from above subtle highlights are generated on the lower lips of the holes.