Ninja is dead but I just want a simple answer on this:
At the time of adding a new coin on the exchange, you can also add a value in your internal database for the max total supply of coins. You can then use this to detect if there are more coins on the exchange than there should be total supply. If this is detected the market is immediately suspended. It would be a very simple check and could be implemented with little effort. In fact you could check this value with the network and suspend the market even before all those coins got put on the exchange. So I believe Bittrex could have caught this if they had better checks. I am not blaming Bittrex, I am blaming the developer but saying that Bittrex should be able to catch these things.
Such a change would be a good precaution and I think it's likely Bittrex will consider adding it. However you don't seem to have grasped the concept of max number of total coins yet. The number of coins in the ANN posting is supposed to match the number of coins the source code will produce. In most cases that number matches, in this case it didn't because the dev lied about the max number.
So a precautionary check like the one you suggest would be a good idea, but the number stored in the database could get out of date. A coin could legitimately update their source code to produce more coins than originally intended, and therefore such a precautionary check could halt trading in a legitimate coin.
It's a trade-off that Bittrex will have to decide on, it's not a completely obvious choice to make (although I think they should add it, the trade-off seems highly in favor of it).
I grasp the concept of total supply, I think it's just that producing more coins than total supply is BS in my opinion and I wouldn't support such a coin that "legitimately" did so. I think Bittrex should add such a check and if a coin is going to make a major change like changing total supply the exchanges should be made aware of it in advance anyway.