Release notes for 6.5 say : “This release deprecates support for interop with IDirect3D9 objects on Windows 7 and later Microsoft operating systems.”
Does it mean that a program built with CUDA 6.0 runtime API and using cudaGraphicsD3D9RegisterResource will not work with future versions of drivers?
Yes, eventually such codes will break (if they use the non-Ex D3D9 objects), on some future driver. The issue is not really with cudaGraphicsD3D9RegisterResource, but with the type of underlying objects, which must be migrated forward to equivalent IDirect3D9Ex types.
This question (and answer) may be of interest, by way of example:
https://devtalk.nvidia.com/default/topic/731389/is-direct3d9ex-interop-supported-/
I believe the issue affects windows Vista as well.