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:
Snore (if the target behind the Substitute is asleep)
These moves will also hit the target through a Substitute but do not deal damage:
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 :)