Maybe it's just me, but I was pretty obsesive when I was cleaning the commercial studio that I used to engineer at.
We often used the cloth style pop filters (not as much to stop the pop, but to keep people back a certain disctance, and to keep the drool off the mic capsules).
After almost every hip-hop session, or session that had a very animated and plosive vocalist I'd Lysol the damn pop filter... and the rest of the vocal booth. My father at one point had undergone Chemotherapy and at the time I had learned from my mother how to sterilize any room more than a hospital. Door handles, chairs, light switches, edge of mixing console, computer mouse, etc... and the pop filter.
The metal ones I'd figure you could spray with lysol or similar, or even put in a dilluted solution of something like bleach or whatever and let it sit for a minute. It's metal... unless it reacts funny with the metal, it shoudl be fine.
Keep in mind, if you aren't healthy in your studio, you probably aren't getting to engineer enough.
David Fisher (aka tibbon)