Each time you get a nugget of ore, a mineral or a branch from their corresponding CNR sources, there's a random chance that the rock/deposit/tree will be used up.
For ores and trees, there's an artificial cap on the yield set at 10 pieces (or 11 if you're lucky, as you said). For minerals, there's no cap, but the random chance of being used up logic applies the same for all.
I think each type (ore/mineral/tree) has its own unique chance of depletion, but I don't have any code in front of me to confirm that.
Edit: Missed a bit of the question...
There's no difference in mining minerals with a chisel or a small pick. Some people swear there is, but there's not. There's nothing really that improves your chances at mining minerals, at least as far as I know. Mining ore and chopping trees are affected most by strength and number of attacks/round, since it's all damage-based. But that doesn't affect yield, just speed of harvest....or if you're able to overcome DR and harvest at all!