My question here is, What happened to the money hackers stole? who paid it?
The hackers didn't steal anything according to the Bitfinex announcement. The hackers would have had to withdraw the bitcoins/litecoins. Maybe they managed to withdraw a few from the hotwallet but the amount (if any) is probably very small and and loss would be covered by Bitfinex.
The main issue is if the trades are not reversed then it is inevitable the hackers will then proceed withdraw their gains when withdrawals are enabled again. It is virtually impossible to determine all the accounts the hackers would have controlled at the time (other than the one which exploited the bug and executed the huge market orders).
Most likely they would have set up multiple accounts and placed buy limits for litecoin at say $16 and sell limits at $22 just before the hack. Then with their main account they would manipulate the LTC ticker exploiting a bug/security vulnerability in the trading engine and place a huge market sell for LTC down to $16 (so their other accounts can buy cheap LTC at $16) followed by a huge market buy to $22 (so their other accounts can sell at $22 with a quick profit). Repeat this a few times as has happened and they would most likely have made a few hundred thousand dollars worth of LTC.
The main account of the hacker executing market orders would be easily determined by the admins and then the account frozen, however the other accounts of the hacker which placed the limit orders would be extremely difficult to determine, unless the hacker was stupid enough to use the same IP's as the main account (extremely unlikely).
The only choice the admins are left with would be to reverse all trades during the period so the hackers don't get away with anything, whilst simultaneously reinstating all accounts that would otherwise not have been affected if it wasn't for the hacks.
Also, many users who would not have otherwise lost or get stopped out, or end up with negative balances would be justified in having all trades reversed. Those trades which made a huge profit due to the fraudulent trades of the hacker will also have to be reversed. There is no way around this. Nobody loses, all accounts are reinstated back to before the attacks. The only people complaining are the ones who lost out on an unfair profit (which should not have been realized under any normal market circumstances). This is fairest solution considering everything and it is impossible to please everyone. There will always be complainers.