Not only am I a bean collector, but a silversmith, too!
Seed-O, the easiest way to attach the shells to the necklace would be by forming a
bail from some wire. Using a bail you wouldn't need to cut the string apart. The bail would run through the shells with a loop on the end that would go around the string; one would look nice hanging down from the center as a focal point. Google necklace bail and you will see many solutions.
If you want to use both horizontally on the string you might want a third object to dangle down from the center of them for balance. You could still run a wire with loops at both ends through the shells, then tie the string to the loops. To drill them out I would put them in a
small jeweler's vise and drill them with a
dremel/flexshaft tool with a small drill bit. You probably don't have these tools, though.
There is an inexpensive hand tool called a
pearl drill or reamer that is basically a handle with a little drill bit on the end. They probably have these at your local bead/hobby/harbor freight store, and certainly online. Drilling a pearl is probably not that different than drilling a bean, as they are a bit powdery inside. It would probably work for the shells, too. If the beans keep splitting, you might coat them a couple times with some sort of acryllic sealer to keep them from coming apart.
You would need to secure the shell/bean in some sort of padded vise though, as it would be difficult to hold it in
padded pliers or a
hand vise with one hand and drill with the other. You might be able to drill a hole in a piece of wood that you could wedge the shell/bean into that would secure it while using a hand drill. Also it helps to coat the drill bit with beeswax or a little bar soap like Ivory as a lubricant.
Hope this helps!