If they aren't windows, then what might they be?
The only alternative that comes to mind is similar holes on the sides of the ship's inspiration, the WWII submarine. A spaceship wouldn't need holes for flooding, I guess, even if she landed frequently on planets with atmospheres. But the flooding function more generally represents the sub coming to an understanding with its environment, i.e. diving; on the BoP, the holes might thus be argued to be a component of the cloaking device.
You inspired me to take a second and close look
at these "portholes" with the obvious analogy to a WWII submarine in mind and I agree.
Some of the bow holes might be torpedo / missile launchers and the plasma weapon launcher in the center could have just been added for the mission we saw in "Balance of Terror".
The in/outlets of a WWII submarine serve the purpose of submerging the vehicle (= rendering it "invisible"), therefore I know believe that the holes on top of the Romulan Bird of Prey serve the same purpose, i.e. rendering the vessel literally invisible.
Just because the propulsion units resemble warp nacelles they don't necessarily have to be those. These have a noticable exhaust at the stern and I already argued in another thread that the nacelle caps of the Enterprise could just be these enigmatic antimatter reactors of the warp nacelles, mentioned repeatedly in TOS.
In this particular case these might just be nuclear fusion reactors which power the BoP's weapon and cloaking device and also provide the exhaust reactants for Impulse Fusion drive.