I started gambling at 999dice the other day using Seuntjies DiceBot. The reason I started gambling there was due to the low edge and because it's supported by the dice bot which gave me some confidence since the dev removes sites that are scams.
I have to admit that I only noticed this thread after I deposited 0.013 BTC. That made me a little nervous, but not super nervous since it was profit I made from another dice site (bitvest.io). After making a profit of ~0.009 btc I cashed out. Zero problems with cash out. My money was sent within 5 minutes.
I think some of the people not getting paid probably tried to do double spend attacks and 999dice preys on these people since they were trying to take advantage. Shady on both sides to be honest, but like I said 999dice has been good to me.
All of the problems with it not being provably fair really is a non issue. The Seuntjies DiceBot dev already confirmed that 999dice is within the statistically normal range when it comes to randomness from a good pRNG.