A lot of people do query under their pen names--after seeing a number of people do that here, that was what I chose to do with mine. I have a blog, an e-mail address, and a slowly growing web presence under my pen, and so if there's the slightest chance an agent might go, "Oh yeah, her!" I'd like to exploit that. Plus it's easier using a separate email for my querying and writing-related endeavors.
The title page included with any partials and fulls has my real name and then my pen name in parentheses above my mailing address.