I just remembered that I left my snap in carper on the boat. It has a cover on it. The carpet its self if all PVC with a rubber backing. Made me wonder, do you take out your snap in carpet?
I ended up not using it this past season so just left it in the basement when I stored for the winter. I've kept it in the boat some years and others not. If it was stored outside and not in a garage, I'd probably take it out.
it's going to hold moisture even if your cover is 100% waterproof--which is highly unlikely. And if it had salt water in it, even worse. remove, store elsewhere, leave it in storage next season and thereafter.