You just need to use a move that isn't blocked by wonder guard (Flying/ Fire/ Rock/ Ghost/ Dark), then the substitute will break, then you'll be able to hit Shedinja.
You can also force it out of it with roar/ whirlwind.
Additionally, any weather buffeting or entry hazards will KO Shedinja on switch in.
EDIT: so you're asking if the substitute will break after 1 super-effective attack? Yes it will. Something like Rock Blast (as suggested) will break the substitute on the first hit, then KO Shedinja on the second hit (unless it's holding a sash, in which case it will KO Shedinja on the third hit).
A substitute will take the damage, no matter how high the damage is, and will fade after one hit if the damage is high enough. While it has 1/4 of the HP of the Pokemon that made it, Shedinja's low defences mean that the substitute will break in nearly all cases.