I just got a 2002 Civic EX, and upon removing the air filter I found walnut husks below the filter. In addition we found a black walnut seed (bigger then a golf ball) just sitting on top of the engine (presumably from a squirrel) when I inspected the car before buying it.

I am a bit worried that squirrels may have stashed more nuts, or even stored nesting material in the resonator. Can you open up the resonator box in any way? Or am I stuck pull the entire box and hosing out the inside to clean it out?

Picture of where the nuts were sitting (this was after removing some bigger husks):

 

If it's clogged up with a nest, you would notice a serious loss of performance. A few shell scraps are nothing to worry about since they are before the air filter anyway. Do check the filter very carefully for any chewing damage, which would create holes and let unfiltered air into the engine. Or just replace the air filter.