Remember than a 12g nanocube only holds about 10 gallons of water when full. Less once the rock and sand is in, so youre really looking at around 8 - 9 gallons of water.
I did a 3g water change today and after siphoning the water out, the level was almost half way down the tank.
Leaving corals exposed for a few minutes is not a problem. Your water change water should be ready to go once you are siphoning out the dirty water anyway.