Yes in Generation VI Substitute no longer blocks sound-based moves. Therefore if the target's Pokémon is behind a substitute you can still hit it and deal damage if you use one of following moves:
Boomburst
Bug Buzz
Chatter
Disarming Voice
Echoed Voice
Hyper Voice
Relic Song
Round
Snore (if the target behind the Substitute is asleep)
Uproar
These moves will also hit the target through a Substitute but do not deal damage:
Confide
Grass Whistle
Growl
Metal Sound
Noble Roar
Parting Shot
Perish Song
Roar
Screech
Sing
Snarl
Supersonic
As of Generation VI a Pokémon that has Infiltrator as it's Ability can hit a Pokémon with a Substitute, as Infiltrator allows you to bypass Substitute.
Whirlwind also bypasses a Substitute like Roar causing the target to be switched out.
Multi-Strike Moves may be able to break a Substitute and continue to hit the target dealing damage. This though depends on the Multi-Strike Move being used, how many times it hits, the type of the Pokémon behind the Substitute, the type of the Multi-Strike Move and the type of the Pokémon attacking the Substitute.
Hope I helped :)