There is no reason to nail into the epoxy. Remember, the nails only hold the deck until the epoxy dries. On the ends of my Patuxent, I was able to use spring clamps to hold the deck at the ends - I was afraid nails would split the wood, or, even worse, go in crooked and come out the wide of the hull.

Some people use straps and packing tape to eliminate the nails completely. So eliminating just the end nails is not a big deal.