When we moved to wiredTiger, we ended up with a bunch of zombie directories. This was related to the desire not to delete those directories when the database that related to them was dropped.  

If we could get an optional flag to send the dropDatabase command to tell it under which scenarios we want it to do the drops, that would reduce a bit of the risk of doing it the alternative way.

SERVER-17703 has this recommendation on the current final comment.

Deleting with a find -type d -empty in the data directory might work, but is less preferable than just asking dropDatabase to do it... especially when we know, as we do in our case, that it's entirely safe to delete any directory for a dropped database.