They are most often called port holes or air ports. The terminology varies with which side of the pond you are located. Also on some pre-war ships that underwent wartime refits the port holes were plated over. Chck your references for the exact configuration for the time period you are modeling.
If they are molded/cast uniformly I usually paint everything the camouflage colors, then go back with a 0.005 inch fine point pen (technical rapidiograph pen or equivalent) and fill them in. Just touch the pen in the depression and give it a twirl. I will also blacken in square bridge windows in the same manner.
If you are going to drill ports where there are none or they have been filled you need to take special care to make the spacing uniform and make them parallel (most likely to the waterline). Also make sure that the hole sizes are uniform and are not skewed with the surface.