. . . and as for 80 odd scupper/drains . . . these should be 1/64 by 3/64 th inch.
Looking at the planking, on the plan. The top two planks are the gunwhales. If it is possible, remove these top two planks, you can get stuff to ease even CA glue. The scuppers could then be filed into the bottom edge of the first gunwhale plank. A jig would make this filing easy.
1/64" is near as darn it 0.4 mm
You may be able to get a 0.4mm or 1/64 drill bit. I know you can get 0.5. At this scale 0.5mm would not be noticed.
You would need to make a jig, and be very careful when setting it up. You could drill the holes at either end and then use the drill bit as a router for the last bit in the middle
Or, thinking laterally.
At 1/64th, these scuppers would probably not allow water to escape, and they would be difficult to paint without fouling.
If you make a small tool with a tip of 1/64 x 3/64 and use it to punch a depression into the wood. This would be easier to place than any jig, especially when following the waterways.
When paining, you could paint into the depression with black first. Then when you come to paint your gunwhales as long as you keep the brush light, you could paint over the scupper, without painting in to it.