Hi Jim this is a difficult one, I have an old (100 years+) pond yacht with drawn planking, I decided much as you have thought and started to remove it. I regret doing this now and it is partly scraped off looking for a better idea.
I recently restored an old (80 years) boat with a pencilled in deck and carefully enhanced the faded pencil lines and a gentle scrape with a sharp carpet knife blade improved it no end. It is what it is!
You could re-plank the deck and that will all be new with an old hull underneath. Is it possible to keep the top of the deck and put a sheet of ply strengthening under the deck? I feel all the holes in the deck are honorable ones and now I just plug with similar coloured wood, making no attempt to hide them.
You can probably see what look like brush marks in the wood, if these are gently scraped off, then re varnish by putting a cotton cloth over a finger and smoothing the varnish, which should be slightly thinned, over the deck do not allow to puddle.
If you do re-plank, in the past I have glued in the king plank fore and aft, and it should be twice the width of the other planks.
Work from the outside coming inwards from deck edge. I think this is the only way to get the most noticeable planks looking correct.
I soak the planks put some pins in and some weight to keep the planks flat, doing both sides one after the other. Allow for drying. I cut the King plank waste from the shape of the deck plank. Look at a photo to see what I mean. the deck plank should be cut at right angles placed over the king plank where it meets.
Measure one third of the width of the plank and note where the king plank edge is and cut down with a sharp chisel blade through the deck plank and the king plank, then cut the king plank at the end of the deck plank, fish out the king plank waste and you should have a perfect fit for the plank all nicely 'joggled' in place.
Pin holes in the planking can be restored by a drop of water over the hole which will enable the wood to swell and hide after a few hours.
regards,
Roy