What kind of glue works for stones and shells?
As both material are kind of mineral, I think the same glue should work on both. The surface must be clean, in other words free of grease and dust. Ethanol or isopropanol work usually well. It will glue better on rough surface, so if it fits in your work sand paper the surface before cleaning and applying glue. For the shell, depending on the type, maybe some vinegar can make it rough (acidity will attack the calcium of the shell).

I am gluing small stones on substrate with cyanoacrylate (Superglue). It is a thin glue, so it won't fill the "holes" between the stones but will be almost invisible and should also stick if the contact surface is small. Time for the glue to set is extremely quick.

If you want to glue and fill the hole at the same time, 2 components epoxy such as Araldit should work and some are transparent. Those glues are usually quite "thick" but you can make them thinner by heating them (with a hair dryer for example) but they will also set faster with the heat.

I also had success gluing gravel on substrate using PVC glue (wood glue, or "colle blanche" in French), but I don't think it will do if the contact surface is small.