Partly because of curiosity raised by this thread and the fact that I had a mouse problem in the garage last winter, I checked my air box/filter arrangement yesterday. Found out two things:
1. The direction of air flow is as DirtFlier says above, and
2. Yep, the mice visited last winter. I found about a dozen sunflower seeds inside the air filter! (They probably couldn't get any more to stay in there because of the vertical alignment of the filter and intake tube just below it.)
In one of my Goldwings years ago, the air box was nearly loaded with kernels of corn after winter. Surprisingly, it didn't seem to affect the way it ran, but sure surprised me when I opened the air box to check the filter!