When a --uri option is used, the absence of the ssl option there overrides an --ssl option on the command line. E.g.

1. will not use SSL: mongodump --uri=mongodb://localhost:27017/ --ssl
2. will use SSL: mongodump --uri=mongodb://localhost:27017/?ssl=true
3. will not use SSL: mongodump --uri=mongodb://localhost:27017/?ssl=false --ssl

Case 1 should use SSL. Case 2 is fine. Case 3 should be an error about conflicting arguments (as is done for other URI/command-line conflicts).