On a carbed bike, can you eliminate the air box with pod filters?
Yes.
Some people have had issues with inconsistent running in side winds, and you need to jet differently than for an open airbox or drilled lid.
No issues at all, including side winds. I've been doing it on dozens of bikes for about 10 years and have never seen a problem. The jetting will need to be at least as rich as an open air box, my experience is that it usually needs to be a little richer. Some people like K&N and others (like me) Uni's, but either way, get the biggest one you can stuff into the available area.
Refer here http://www.ducatisuite.com/jetkit.html (http://www.ducatisuite.com/jetkit.html)
JM