Yes. WonderGuard only prevents direct damaging attacks - which means moves like Simple Beam, Gastro Acid and Soak will all affect it and abilities like Iron Barbs and Aftermath as well. Any damaging weather/entry hazard will work past Wonder Guard.
Mold Breaker nullifies certain abilties, with Wonder Guard being one of those. Mold Breaker along with it's variations Turboblaze and Teravolt will nullify Wonder Guard and render Shedinja completely and utterly screwed
~Hope I helped