Hi Colin,
I wish I could help with the pebbles to make a hole so small without breaking the drill bit seems impossible to me probably because I'm so heavy handed, for small holes I think they now blast through with high pressure water/air.
However I can suggest Soapstone which you would be able to drill through and then turn or hand carve into the desired pebble shape, the pic below is turned from soapstone, a bit dusty but very easy to use. It also comes in a number of colours.
Cheers Martin.