The plywood remains somewhat porous, almost like a deck sealed with Thompson's water seal, but it does repel the water. My decks were never shiny and slick. I have seen the epoxy bartop finishes on some restoration thread floor sections. I don't know how they would hold adhesive, looking like a piece of glass. My adhesive (from Lowes, with the outdoor carpet stuff) held the carpet quite well, and pulling it up was no treat. I belt sanded the high spots, and spread more of the same adhesive, before putting the vinyl down and it is staying put quite well.
I would recommend wrapping floor pieces if using vinyl. I have a seam that is fine most of the time, but on really hot days there is a small wrinkle in about a 3 inch spot, where one of the deck boards is moving some and the other is not. I am sure if I ever get a crack it will be right there. I didn't see it much this year, so maybe the floor and vinyl are getting along better as time passes.
Doing it again, I would replace the Lowes outdoor carpet, with more Lowes outdoor carpet, not Vinyl.
Lowes carried the vinyl, but Defender had the Nautilex at a great price so I went with that.
Some guys go at this restoration stuff like they are building furniture, and their boats are works of art, more power to them.
I took a worn out boat and made it a very nice looking fishing boat, (with less than $3K total invested) which is exactly what I was looking for. I pulled it out of the water in December and had it back in in April.
To get back to the original question here. On a low speed, small wave lake, I don't see any reason why you could not use vinyl deck boards to re-deck a pontoon boat. Use plenty of stainless fasteners, and try to make sure you get adequate support, or replace the lost support provided by 4x8 sheets of ply on the current deck.