These screws are cheap carbon steel, with a very thin layer of plating. If left in the wood and exposed to water - or, far worse, salt water - eventually they will start to rust, and the staining will discolor the surfaces. There is no way of getting rid of this marking. In fact, it just gets worse with time. I've seen a case of a beautiful classic carvel yacht which was extensively refurbished, but they left the original iron fastenings in her. After a while, the rust weeped through the planking, and the boat was essentially a write-off. You'd need to use marine grade stainless if you wanted to leave the screws in. However, the screws go right through both layers, and protrude well inside. In which case they'd need to be ground off. And the screw heads would need to be countersunk. A lot of work and mess and heat. Much better to take them out. They contribute very little to the overall strength.

Thanks! None of these planks actually required spiling but if I'm doing it another day I will make a video to show it.

These came from Robbins timber in Bristol.

They came straight from the supplier (Robbins Timber) finished to 5x90mm so all I had to do was mark out and drill the screw holes. Where two boards met I cut a 45 degree angle on the end of each so that they would glue together better.

I don't think so. The outer layer of planking is a close fit on top of the inner layer (which is fair), and any remaining space between the layers, which would only be a fraction of a millimetre, is filled with thickened epoxy, with the excess squeezing out at the edges. This is just a variant on the cold moulded method used for dinghys, e.g. Firefly and Albacore, when Fairey Aviation switched production from aeroplanes to boats after WW2 (although they used Resorcinol glue, which is not a gap filler and has to be autoclaved). I saw an Albacore in good shape only a year ago!