You all are proving my point that it's overblown. Out of 19 responses, only three people including me have said not to worry about mice. That is ridiculously out of proportion to what you see on the trail. Almost every single hiker I knew on the AT would and did sleep in a shelter in a heartbeat if they knew it wasn't going to be crowded or if there wasn't going to be a snorer or a creepy guy in there. People are the animal that force hikers out of shelters more than anything else--no one talked about mice after the initial jitters in Georgia. In fact, after spending five months on the trail (and yes, I recognize that many commenters have more experience than me on this count), the only time I heard of someone's gear getting eaten by a rodent was my friend Foon who was sleeping IN HIS TENT when something nibbled through his food back and one sock. He somehow managed to survive this catastrophic turn of events.
If all we have to go off of is anecdotal evidence, then mine says: Me and my friends slept in AT shelters constantly for five months. We never had problems.
Also, the hantavirus thing is a grossly misplaced fear. Hantavirus infections have shown up on the East Coast, but the vast majority of them are in the arid and semiarid parts of the West because mouse poop needs to dry and aerosolize really fast (48 hours or less) before the virus dies, and then be breathed in by humans. The East is most of the time too humid for humans to contract it. The rate of infection in humans is also minuscule. There was one case of hantavirus for every 175 West Nile cases diagnosed last year. One case of hantavirus for every 800 of Lyme disease. I will continue to sleep soundly in shelters on the AT knowing that I am more likely to get mauled by a wild boar in my sleep or have ball lightning sear a hole in my abdomen than contract hantavirus. If you're going to go fear-mongering about a disease, at least read up on the likelihood of anyone on the AT contracting it first.