You've misunderstood how Shatter works.
You only have one of two options when casting the spell:
1) Area of Effect:
Used as an area attack, shatter destroys non-magical objects of crystal, glass, ceramic, or porcelain. All such unattended objects within a 5-foot radius of the point of origin are smashed into dozens of pieces by the spell. Source (PFSRD)
This only effects unattended objects and therefore would not effect anything your alchemist is carrying.
Alternatively, you can target shatter against a single solid non-magical object, regardless of composition, weighing up to 10 pounds per caster level. Targeted against a crystalline creature (of any weight), shatter deals 1d6 points of sonic damage per caster level (maximum 10d6), with a Fortitude save for half damage. Source (PFSRD)
This may only target one object, or one crystaline creature, so doesn't affect the Alchemist.This part of the description doesn't mention whether or not the object must be unattended. Your DM could rule that one attended object could be targeted but then it would still be granted a save, using the Alchemist's Fortitude or Will (I leave this to DM discretion because this doesn't seem like the intended effect of the spell). All in all, if you're DM allows it, using Shatter against an Alchemist would not be much different from sundering a Fighter's weapon.