Black pearls are hidden in locations as regular hidden objects. You can only find one pearl per search, and they can't be found with Seeker's tools.

Pearls are not on the list of items you need to find, so if you find a pearl after finding all of the hidden objects, it won't count. You also have to complete the location successfully in order for a pearl you have found to count.

The pearls you collect aren't displayed in the Inventory, they go straight to the counter in the Guardian Quests window.