If they are picked up along the seashore, then I don't see why it would be a problem. They were discarded by the creature when it died or no longer had a use for it, so the creature isn't being harmed.
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.
As I understand it, @Citrus333 is correct. Most shells found when the original owner is no longer there are worn or partially broken. The best-looking shells (offered for sale) were probably collected when the animal was still alive. I don't see a problem with collecting shells at the seashore, though; just make sure nobody (like a hermit crab, worm, or whomever) is still home- old shells are sometimes used by critters who move into them.
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