The dual GPU support is unofficial, so to say. It means that if something doesn’t work with multi-GPU, there’s room to report it, but not to complain about it. However I have been using 3 5970s in one machine (for a total of 6 GPUs), and they work alright. I have not encountered any problems with them. Something however must not totally work, since the support is not official. AMD employees are not allowed to talk about bug intimacies, why they arise, all that can be told is that dual GPU cards utilize internal CrossFire connection, which is most useful for games, but we all know that both SLI and CrossFire have to be disabled to do GPGPU. There is some internal optimization that is hard to come across with software solutions. If you read AMD forums, MANY people have been complaining about dual-GPU support being unofficial, and it was planned to be resolved this March-April (SDK 2.4). However the solution was not ready, so very much likely the SDK coming this August-September (2.5) will inlclude the support.
AMD APP SDKs has been released on a 6 months basis (for the past 2 years now) and it is planned to keep this track. Drivers are released every 1 month, and all SDK features and bug fixes in drivers are based on user/programmer demands. If you would chose to buy 6990, I would advise reading a little through AMD forums.
Anyhow, the chioce is yours. Single GPU cards are sure to work (from both vendors of course), and dual-GPU cards on AMD side might take a little foruming to get to work. Driver fixes come frequently, SDK fixes (and new features) come every 6 months.