'Morning, Joe; Welcome, by the way!
Joe, are you talking about plastic laminate (Arborite), or wood?
If you mean plastic, then you should probably screw
down the plywood, and make sure the heads are slightly countersunk, whichever you use...with nails there's always the risk of them working their way back up slightly, and with the weight of someone walking on the deck, breaking through the laminate.
If you were thinking of wood
laminate, don't. There's no place for wood laminate where there's water. Baaaad combination!
If you want to level off the countersunk fastener holes, just use autobody filler, and sand flat after it cures. The stuff comes in small cans and is pretty cheap...and waterproof. Contact cement doesn't really need to penetrate the substrate if the surface is impervious, so sealing the plywood is probably good insurance considering the water issue.
(35 years of dealing with water damage in peoples bathrooms has made me paranoid about water.