Your nails will reveal.

Why can't we use screws and countersink slightly?

Mine left bumps - I'm still kicking myself for not using a nail set to drive them flush (or slightly beyond flush) - but I doubt anyone other than another boat builder will notice - it's not that bad - but it is noticeable if you're looking for it.  I was hoping the glass would cover it up, but it didn't.  I'm too impatient to continue to build up epoxy; If I were painting the deck, I'd use some fairing compound on it.

I did use a nail set but still had some slight bumps. after expoying and then sanding the epoxy and then put on some trim paint the bumps disappeared. 

That said, you are probably the only one who will ever notice. perhaps its time to apply the 3 foot rule.  I'm sure it will not affect how the boat paddles.

Ed 

although it is not acutally a nail set, I found a tool that almost exactly fits the head of my deck nails and sets them just below the surface.  The tool is actually intended to hold the nail inside a tube and you put the tool into a tight spot where you could not get your hand to hold the nail and then you hit the end of the tool and a rod inside the tool pushes the nail into the wood.  There are various sizes depending on the nail you are trying to drive. 

We tried to drive the brass nails with it but the nails tended to bend so we just drive them the regular way and then countersink them with the tool.  If you want the nail heads to have a bright finsh you need to touch them with the sand paper before you set them down.