I found on MongoDB mailing list one use case for
The count() command is generally an estimate of the current document count, based upon statistics provided by the storage engine.
After an unclean shutdown of a mongod using the WiredTiger storage engine, count statistics reported by count may be inaccurate. If this does occur you can run validate() on each collection to restore the correct statistics.
are there other use cases? Maybe regular DBA job task? We have regularly unclean shutdowns.
The validate command checks the structures within a namespace for correctness by scanning the collection’s data and indexes. The command returns information regarding the on-disk representation of the collection.
The validate command can be slow, particularly on larger data sets.