Mice can be a problem if they get into the food and may carry disease but if there is no sign of infestation I wouldn't worry too much about it. Keeping bugs and moisture out of the food can be done by using an airtight resealable container and only having one or two day's worth of pellets and hay in the cage at a time. If bugs do get into the feeder they can't take up residence in there. I'll usually fill my feeders at night and in the morning with a scoop of pellets.
I store my food in a rigid container with a rubber seal in the lid and I am very pleased with it. These can be found at places that sell kitchen stuff.
I have one chinchilla in my room and I don't notice any smell at all from his cage. I empty the cage pan about once every 10 days, scrub it once a month, and sweep out the cage about twice a day. With two chins you'll have to do it more frequently like Jamie said, at least once a week. Urine on wooden shelves can add to the problem but that is solvable if you add a small pan of bedding or clay cat litter that will make a different spot more attractive for the animals to urinate on. Once they get used to using that spot they'll usually continue to use it even after the pan is removed. Chances are if your cage stinks it is not a healthy place for your pets. Compared to other animals I've kept chins are odor free.
If the problem is noise there's not much you can do there. I leave in one hanging toy and remove all the loose toys and things at night and it helps. It probably isn't too great for the chinchilla to do this but I don't have much of a choice. He still has his shelves and a small toy to chew on to keep his teeth trimmed. Also I have made sure everything in the cage that rattles is either bolted or wired in place. I use a 1" c-clamp on the door at night since it rattles without it. His squeaking sounds don't bother me too much but the thumping and banging sometimes do. By taking these steps I can sleep well most nights. If I had a basement I'd be tempted to keep him there because of the noise but it would be harder to interact with him. Putting a second level on the cage is a big plus though. I don't think it's a good idea to keep two chins on a single level.
Those are my thoughts.