depends on the shelters.
Heavily used ones will be infested with with mice
They are dirty, have mouse droppings (and dried urine as the little buggers are incontinent), and are best avoided IMO.
When sleeping in one, you want a groundsheet or tyvek or polycro under you to keep your stuff clean and disease-free.
Even tenting close to AT shelters in the spring you will be attacked by mice looking for a free meal. They have been conditioned by the others that came before you.
Dont know about the ones on the OT if thats where your headed, it sees a lot less use.