No negative from me. I've had a winter hoop house for two winters with no squirrel damage. And we have squirrels. Lots and lots of very brazen, vocal squirrels. Little buggers decimate my strawberry patch every Spring which sits right next to the hoop house. This year I'm making some protective structures to fit over my new strawberry beds so I'll have their number.

However, it's also possible that what you put in the hoop house might possibly have an effect on how determined they are to get inside. Mostly I have bell peppers in there which they probably aren't keen on.