Well even if all the users deposit at once (which is highly unlikely) they simply give to every user the other users bitcoins so they should never ran out of coins... they get 2000 BTC with your example and they need to give out 2000 BTC so they don't even need to use their own supply!
You're missing the one thing that makes ChipMixer unique: the coins you get back are older than the coins you deposit. That means ChipMixer doesn't just use my deposit to pay you, and your deposit to pay me.