EDIT2: ALso, please take this with a grain of salt; this is a purely hypothetical answer, or a guess. There may indeed be a clear hardware-based reason why 64 is the maximum. Frankly I don't know, and my answer is based on an assumption that there is no such hardware limit, per se.
It's probably a combination of three things: first, there is a limit to the number of threads which can be resident inside a block; second, block dimensions are typically in multiples of 32, and even more often in powers of 2 greater than 32; third, coordinate systems used in the solution of multi-dimensional problems are most often oriented so that you're looking at the scene directly (i.e., with the important bits more distributed in X and Y than in Z).
CUDA naturally has to support 1D access, as this is an immensely common and efficient access pattern when it is applicable. TO support this, the X dimension must be allowed to vary over the entire range of 1024 threads.
To support 2D access, which is less common, CUDA should minimally support up to 512 in the X dimension (using the convention that the X dimension should be oriented in the coordinate system so that it measures the biggest spread) and 32 in the Y dimension. It must support up to 1024 in the X dimension, and I suppose they relax the requirement that the X dimension be no smaller than the Y dimension and allow the full 1024 range of Y values. However, in my understanding, 32 would have been plenty big for the Y dimension maximum.
To support 3D access, maintaining X, Y >= Z and trying to reach 1024, it seems to be that in the best case X=Y=Z=10; so there's no real argument for allowing Z to be greater than 10, given my assumptions
In summary, I don't see why they couldn't have made the maximums (1024, 32, 10). My question is why make them (1024, 1024, 64)? The only answer I keep coming back to is to allow some flexibility to programmers to violate the X>=Y>=Z coordinate system convention.
Edit: given my summary and hypothetical answer, the real answer to your question is this: it's an arbitary decision.