I'd leave the drain plug hole. There WILL be water in there eventually, usually from condensation.
I've had a couple of disasters with expandable foam, including at least one exploded boat, and about a dozen boats where the foam became saturated with moisture over time.
Not much danger of the former if the deck is off. As for the latter, I am told that modern foam formulations are much better about absorbing water. All of the water absorption I've seen came after 10 or 20 years, so who knows. The expanded foam in Jeff's boat sure looks beautiful compared to the motley collection of insulation foam in my boat.