It seems likely to me that eventually blu-ray movies with 3D will only have one disc at retail. It includes both the 3d and non-3d versions (as the 3D discs have now), and will include the extras/bonuses found on the regular disc. Instead, they may drop a few of the language tracks to make room for the 3D version, and they'll have more international SKU's rather than having one SKU for 3D and on SKU for 2D.
Could be years before this happens though. But if (when) it happens, you'll be able to get the 3D versions from Netflix or any other rental channel, because it will be the only version available.
My question would be can the 3D version of a movie be streamed through Netflix? Or could a 3D version be purchased through the Playstation Network video service?