The lower row at the bows were plated over - see the photo attached, where DoY's lower deck bow scuttles are uncovered just prior to being broken up.
I spent a LOT of time a couple of years ago staring at as many photos as I could to determine the scuttle positions for King George V, Prince of Wales and Duke of York. All three ships share most of them in common positions, but each ship has some unique positioning as well. A noticeable feature on Duke of York is the upper row of scuttles aft of the armour belt are set slightly lower than the rest on that deck. On both KGV and PoW the same scuttles are at the same height as the rest on that deck. However, the round scuttles on PoW in the same positions as the rectangular deadlights on KGV occupy the slightly lower positions as per DoY.
I have made it as far as modelling all of the different positions into my KGV hull (and note also the Prince of Wales bow shape is very slightly different than the other ships of the class, right at the very top - narrow vertical band). I have NOT yet got as far as blanking off any of them, but they were all present in the hull.
These are the results of those efforts, port and starboard for each ship (they are not symmetrical) [also all deck and superstructure features are for KGV 1941, regardless of hull in these renders - and even then a lot of it still needs reworking]. Lighting/reflections at the stern on the starboard side images makes some of the positions harder to spot:
Not sure if Prince of Wales ever had any plated over; KGV had several plated over, most likely in refits; DoY may have had the lower deck scuttles plated over by the time she was launched? Haven't seen many early DoY photos so I'm not certain on that last point.