Para remover o subdocumento, use $pull
Esta consulta será removida do subdocumento aninhado
db.collection.update({ d : 2014001 , m :123456789},
{$pull : { "topups.data" : {"val":NumberLong(200)} } } )
db.collection.update({ d : 2014001 , m :123456789},
{$pull : { "topups.data" : {"val":NumberLong(200)} } } )