Scattered thunderstorms are usually in the afternoon, and only last an hour or two.
When a storm approaches, you have time to leave the park, or find shelter in a restaurant.
In your case, I'd say hotel room, rest, then come back. If you're not tired, then City Walk for happy hour.
Not sure if Spiderman and Cat In the Hat run, but even if they do, you'll be stuck in a gift shop when you exit if it's pouring. I'd rather be slamming beers in my hotel room.