Why not?
Remember, you don't just 'double the number of shader cores' - the entire GPU must be scaled up to prevent one aspect bottlenecking the data flow. if you double the number of shaders then you need, in principle, to double the number of TMUs, ROPs, cache, interconnect logic, etc. If the memory interface width is also increased, then the new GPU will be not too far off double the number of transistors. Usually it will take a few extra transistors to support the increased complexity of the GPU, but an architectural redesign can often negate that.
Take the example of the 4870 -> 5870: Here we saw a doubling of the number of stream processors (800 -> 1600), as well as a die-shrink (55nm->40nm). The number of transistors increased by 2.24x: From 956M to 2150M.
If anything, I would have expected a 1024-shader Kepler card to be at least 6Bn transistors, perhaps closer to 6.5bn.