There's no way to tell if the shells were taken with the "owner" or without. Most shells in gift shops (though not all) are, indeed, "harvested" with the animal alive. Some are used for food (abalone, scallop, etc.) and the shells sold for additional profit. If the shop owner claims they're all found empty or dead, the shop owner is lying. It's simply not possible to know.
And yes, any time we take animals, it harms the environment.
As for shells (just shells) along the shore...they are part of the environment and over time they create sand and provide nutrients for plants like sea oats and mangroves. Picking up some shells is likely harmless, since we seldom pick up the broken or not-so-pretty ones.