Topic on Engine talk:Source
I am not aware of the specifics that RTSS uses to identify D3D9Ex other than it not being really extensive (since it frequently misreports games), but it does seem that it is even less extensive than I initially thought...
I have confirmed your findings using two native D3D9Ex FlipEx games:
Kingdom Under Fire: Heroes - Misreported as D3D9 by RTSS. Hotline Miami 2: Wrong Number - Correctly reported as D3D9Ex by RTSS.
Well, this is annoying... :(