Removing Database from sharded cluster in Mongo DB
Unfortunately there is some stuff that will not be cleaned up through dropDatabase. On the other hand if you delete it by hand may not will be harmful. Some data like statistics will reside on your nodes anyway till the restart of mongods. (Try it out first! Not on the production), as the configuration database is relatively small and does not have huge requirements in terms of performance, that maybe even not a problem, just to be on the safe side and leave them as they are. 

Also something to check out how to make the manual actions:
https://stackoverflow.com/questions/9407838/mongodb-dropdatabase-not-working

and as it is mentioned on this question the dropDatabase in such case a bit bugy:https://jira.mongodb.org/browse/SERVER-4804