You'll need rivets but maybe not in the quantities they have to offer, (100). You also have to rivet the side panels to the support shelf but you can use the same LF rivets you get for the decking. When I ordered I got an assortment of solids and blinds, counter sunk heads, regular heads in a couple different lengths, I also needed a couple hundred 5/32" for the cabin and gunnels. So that's why I shopped there but you may be able to find what you need at Amazon.
Remember you wont have to worry about countersinking all of the rivets, the ones around the edges are behind the side panels, only the ones out in the ply seams will be seen or walked on. I'm not so sure how well wood putty stuff will hold up or even stick very long to AL, I would hate to have it come loose under there and be a lump. I saw where a guy had used a sharp forstner bit to make the counter sink, then used his left over gluvit to fill the voids and a bondo type rubber spreader to work it in. Once the gluvit cured it was sanded smooth.