I've read that there are ways to script the Dawnguard assets, so that they only show up if the Dawnguard files are present.
http://www.creationkit.com/GetFormFromFile_-_Game#Examples, I'd imagine?
http://www.gamesas.com/user/791299-bw117/: If you need to edit cells, you're probably better off adding Dawnguard as a secondary master. The engine has no problems with ESP masters, but the CK won't allow it. Make a copy of your ESP, open it in WryeSmash, R-Click and copy to ESM. Then open up your ESM and Dawnguard simultaneously with no active file, saving the edits as your Dawnguard supplement. Once it's completed, edit the masterlist of the result with WryeSmash to look for the ESP version rather than the ESM and all will work in game. If you need to edit the supplement with the CK, you'll have to repoint its masterlist the the ESM version and back again.