To see shells and pearls deposits, you need the idea "Jewelry" triggered or researched.
Shells are a naturally occurring resource in Ymir. Shell Deposits are rare and occur along bodies of water, or rarely in mountains and deserts.
Shells are gathered by flint collector, from Porkoderthalian warriors or events.
Shells are required to complete certain quests and researches and can be used to make Adornments.