I think you're probably smart enough to look around the web to see for yourself which is going to be quieter (most important), cooler, and an overall better experience to live with on a day to day basis. The funniest description I read of the 6990's noise compared it to a "squealing piglet". Tom's Hardware said to "think about all of the conversations you can enjoy not hearing". But like you said, the HAF X case is tailormade for dealing with heat and noise producing SLI setups.
So to answer your question, we can look at results from Guru3d, who have compared the GTX 590 in SLI and the GTX 580's in tri-SLI (with the 6990 Crossfire thrown in for kicks):
http://www.guru3d.com/article/geforce-gtx-580-3-way-sli-review/
http://www.guru3d.com/article/geforce-gtx-590-sli-review/
http://www.guru3d.com/article/his-radeon-hd-6990-crossfire-review/
Noise (vs. single card)
580's: 48 Dba (+7 Dba)
590's: 44 Dba (+3 Dba)
6990's: 50 Dba (+4 Dba)
Temps (vs. single card)
580's: 87c (+13c)
590's: 85c (+6c)
6990's: 90c (+5c)
@2560x1600
CODMW2
580's: 199 fps
590's: 161 fps
6990's: 125 fps
BFBC2
580's: 116 fps
590's: 120 fps
6990's: 144 fps
Dirt2
580's: 138 fps
590's: 155 fps
6990's: 153 fps
FC2
580's: 156 fps
590's: 145 fps
6990's: 171 fps
Metro 2033
580's: 56 fps
590's: 62 fps
6990's: 61 fps
Anno 1404
580's: 116 fps
590's: 87 fps
6990's: 117 fps
Crysis: WH
580's: 81 fps
590's: 80 fps
6990's: 84 fps
Average FPS
580's: 123 fps
590's: 116 fps
6990's: 122 fps
BOTTOM LINE:
The performance is pretty much the same. There are clearly some games where early drivers are impacting performance. Fortunately, Nvidia has already released at least two new drivers to address performance issues (AMD has been stuck on the 11.4 Preview drivers for several weeks now). The choice, therefore should fall on aesthetics and particularly noise, with the GTX 590's being the quietest (and coolest) of the options. Oh, and of course, the two GTX 590's will be considerably cheaper.
On the subject of drivers, Hardware Heaven did a review with the old drivers and one with the new drivers. Here is what they had to say:
"So how does our experience with the overclock and new drivers affect our feelings on the value of the GTX 590? Earlier we stated that it was a card which felt a little overpriced, the performance was not quite there and driver issues in games such as Shogun 2 took the shine off the card a little. With the latest driver and running at the maximum performance when compared with the 6990 we are happy to report that the GTX 590 now feels a lot more like it is priced appropriately. We get exceptional performance, improved drivers, cooler operation than the competition, significantly quieter operation too... and of course all the benefits of surround gaming, 3D Vision, PhysX and CUDA.
http://www.hardwareheaven.com/reviews/1140/pg1/point-of-view-nvidia-geforce-gtx-590-oc-vs-radeon-6990-oc-introduction.html