No, but you don't have to add the MP3 versions to the database if you're adding the Flac, if you take some care in how you organize your files and how you let Slim Center scan for music.

Groups of tracks make up an album and Slim Center will not exclude tracks from such groupings based on their format. If you had all your music in both formats it would likely make it easier to omit one format completely from the DB. But if you only have such duplication for some content, then it's a little harder.

There's probably one or more people in the Slim forum with such a setup though, and perhaps they've come up with a decent solution, including the possibility for some plugin to take care of the details for you. http://forums.slimdevices.com