I have pondered the function of this as well. Currently my deck is going back together (new foam core) and there is no backing plate in mine, just a rain leak like you have. BTW, these holes are not sealed from the coring- you probably have rot developing around that hole. It appears that the only possible function for that bolt is to provide extra support for the foredeck without adding an arch below.
I'm building a new bowsprit at the moment and may put in a new "pin" or not. If I do, I will drill an oversized hole in the foredeck (1 1/2 inch or so) then fill it with epoxy and cabosil before drilling the final hole.