Shortly after I purchased a Lexus ES300h, I started noticing mouse droppings inside the car. Finally, one day I opened the trunk and found the whole family running around! I live in rural Nevada (high desert) and park outside under a carport. I had heard stories that Toyota had changed to soy-based foam for the seats, and that this attracted rodents. An acquaintance reported that mice had eaten the inside of her Prius seats and cost her thousands of dollars.
I looked for entry points, but was unsuccessful. However, a friend mentioned that animals don't like the smell of fabric softener sheets - the kind you throw into your dryer to soften clothes. I purchased a box of these with a "Mountain Breeze" smell, distributed some sheets under the seats and put the open box into the trunk. Total success! After about two years, I noticed the turds again, so replaced box of fabric softener sheets, and no more turds.
I'm not sure how this will solve under-hood damage (which, luckily, I don't have), but certain odors definitely deter rodents.
- John Atwood