(Note: I'm one of the closed beta testers, so my suggestion correlates to the beta, not the "classic" version)
When crew mine resources out of asteroids, instead of the entire section vanishing just the ore should disappear and the rock remain intact. I personally think this would look nicer than there being holes in the rock as that would imply the crew drilled through the entire asteroid. The mining laser would still destroy the rock.
Mining ores out of asteroids