There should always be enough coins because shorting is limited to the exchange if it exists at all. The ones at risk of being liquidated are the holders of short positions.
this is an additional risk to the normal riks in putting coins in an exchange.
If the exchange maintains 100% reserves there isn't any additional risk. If a fractional reserve system is used then there is additional risk. An exchange isn't a bank and it shouldn't be using a fractional reserve system. If they are, then you have so many more risks than short selling that it really doesn't matter.
Anyway if you don't like program trading, you are free to start your own exchange not allow it to happen. No shorting so bots. You can set most of the rules you want. It still won't stop the pump and dumps and you will still have coins like AUR losing value over time.