I understand to store Isomalt it must be in a storage container with silica gel packets to extract moisture, but what happens when you actually come to use your Isomalt pieces? do they just go cloudy as soon as you get them out and put them on the cake?

Look for an edible shellac spray.  I've used one from Chef Rubber,  I think there are a few brands, PME, Evil Cake Genius, etc.  

Just spray the pieces well all over and it will seal them.  I used in for a sugar eyeball for a cake of Book from Hocus Pocus and it never got sticky. It was stored in the fridge as well.

They might not get cloudy immediately, but once they are on a cake and moisture gets to them, they can get sticky and possibly melt.