I've had this issue too. When I opened up my air-box after a few months after I got the car I found nut shells and turds in there. Seems to be a popular place as it is easy to get into, secluded and "protected" and it's warm from the engine heat. So rodents will definitely go in there, and even if it's left outside in winter, it's still "protected".

When I store the car, I remove the filter and cap the intake port and exhaust with tin/aluminum foil. Secure with a rubber band. They HATE that stuff and don't chew through it.

Dryer sheets (fabric softener sheets) supposedly have the same effects as moth-balls but without the repulsive smell to us. I place plenty around in the engine bay, grill, interior, and trunk. Anyplace that might attract an unwanted guest. Use LOTS of sheets. Last winter I didn't have that many in the engine bay and a critter made a home in one of my reservoir socks.

Put plenty around the area by the cabin air intake too.

 

As an additional note, be VERY careful about starting your car if something has crawled up your exhaust or gotten past the filter in the intake. My cousin blew up an engine because a critter built a nest INSIDE one of the engine cylinders.

 

I just found some spiders inside the car when I started it up and roll it out the storage yesterday. Scary scary...you saw spider silk dropping infront of you while driving. It scaried the shit out of me.

 

Get spearmint gum wrappers and throw them around in your car. Spiders (and ants) hate spearmint for some reason or another.

My mom used to drizzle spearmint oil by doors and in room corners to keep the ants out and the spiders from spinning webs.

 

Oh yay, i cant wait to find out what made a home in my car CAI FTW!
Then again, whose to say some animal didn't chew through the filter and climb?

If in the exhaust, lol fkn burn.