i've recently discovered how useful sun-drying knicks can be in the prevention of saddle sores - I presume the UV does the job on the bulk of the nasties living in my chamois. we're fortunate in my part of australia to have more than enough sunlight that i can do this all year round. not sure how you NH guys survive the winter with your junk intact...
I assume microwaving your shorts would do the same trick? Microwaves are pretty effective at killing bacteria. Just don't put them in there fresh out of the wash. The water may start to boil and ruin the pad, depending on what it's made of.
This is all purely theoretical, of course. But I know it works with sponges, so why not shorts?