Graf Spee and Prinz Eugen likewise look quite impressive - I didn't realize how much beefier the cruiser was than the pocket battleship.
And I see what you mean about the gaps created by the wooden deck - though the planking is 'way too beautiful to pass up. My first instinct: wood putty filler. With some careful masking, and color-matching, I would think you could squish it in and then, after it hardens, scribe in short continuations of the planking joints, right up to the cleats, vents, etc.. A lot of work, but the result should be awesome.
Keep up the great work, and keep us posted, buddy!