I will help you with that dilemma. Good thing I know some MC.
The mysterious shells are used for trading figurines. Go to Hyrule Castle Town and head to the lowest left of the town. There are manyw ays to get there,
A) Be in your minish form and talk to the dog blocking the road at the south-west of the town. After you talk to him, he will move about so you can pass.
You can swim there as well, provided you have the flippers.
C) Go to the town' milk bar and shrink yourself there. Exit the bar and head towards the little bridge found near Swiftblade's training dojo.
When you have reached the southern part of the town, you will find a tree with an entrance, enter it and Carlov, the figurine maker will be waiting. He will offer you a trade, mysterious shells for figurines.
If you collect all figurines, he will congratulate you or, if you beat the game, you will receive the carlov medal.
The other benefit is, that once you have collected all figurines, you will find a man outside the milk bar. He will unlock the door to one of his shops in the town, namely the shop you can't enter(Though you can enter at the back to see 3 chests a heart piece and a Phonograph)
Hope I helped. Don't forget to Rep.