if you can get some vinyl for free or close to free, it might make it a bit easier to clean and help reduce wear on your plywood floor, and so be a good choice.
If you want to use anything to clean the coop (like a pitch fork or very pointy rake) you might want to avoid vinyl since something pointy used with force would tear it up quickly.
I think painting the plywood with paint from the "oops wrong color" at your local hardware store, or using extra paint from your house is a great way to help protect the plywood a little more.
the sand will wear through the paint layer over time, but I don't see that as a big problem. The sand would do the same with vinyl (slowly wear through the top layer), but if the vinyl is free or cloe to free, then it would be a good way to protect the plywood floor.
If you have a concrete slab, and want to use sand, I wouldn't bother putting any paint or vinyl on it.