
Usually, trainers will give their pokémon special pouches to hold their items in (unless the item can be held or worn in-battle). Sometimes, these pouches are designed to match the color of the pokémon in question. Custom orders of such pouches are incredibly popular, especially on independent artists’ Shuppetsy storefronts.
Alternatively, some pokémon actually have thick enough fur or rolls of fat (it sounds disgusting, I know) to hide smaller items, particularly everstones.