The habit of cracking the knuckles is usually short lived. The kids seem to go through it for a while but it doesn't last.
I haven't seen it do any harm over the years.
Cracking the knuckles is NOT the same as the vertebra cracking when adjusted. The noise is from the same mechanism but that's about it.
For the most part when a spine is mechanically correct it's very dificult to get it to pop. And if it does, if you're doing the right movement, it means the vertebra are moving back into place.
But any structural trauma will cause the spine to pop also. Then you'll need an adjstment or two.