There's no magical solution to this problem. The general rule of thumb is that if it only stocks 1 or 2 at a time, it should be worth something. Should being the operative word here - because certain site events may affect an item's actual market price, despite its rarity. The key is practice and knowing what is worth something, unfortunately. If you haven't been playing for long, I suggest an easier shop to practice at, such as Food or Books. Plushies tend to be "throwaway" prizes from site events and once their value drops, they don't go back up (since they aren't one use). Sometimes even coloured plushies won't be worth much since they were given out during one plot or another.
Another thing I used to do was look up a shop using an Item Database, such as JellyNeo's, to have a general idea of which items will be worth something. Of course you can't memorize the entire list, but you can see things you can be on the lookout for. Unfortunately restocking takes a lot of practice and patience to get the big profit items, it took me years to not keep buying worthless things :P