When I had kayaks I got cockpit covers for them.. like a skirt but no way in. Like you, I had to store them outside. I put the kayaks under a deck and forgot about them until next spring. To prep for winter I washed out the inside, made sure the hatches were empty, made sure they were completely dry, covered the cockpits, and bob's your uncle. Now I have canoes. I store them upside down on saw horses. No prep, no cover. What you should NOT do is to let any kind of tarp rest directly onto a fiberglass, kevlar, gel-coated boat for long periods when there is a lot of sunshine. Boats can easily de-laminate from that method.
No mice ever went into my cockpit covers but during the same periods they managed to visit inside the house more often than I'd like.
"If I'm not going to catch anything, then I 'd rather not catch anything on flies" ... Bob Lawless