For Ephus, X series boards are indeed now our recommended board option, especially PCIe-6321 and PCIe-6323.
For ScanImage, you can and definitely should use an X series board for the ScanImage secondary board (if using Pockels or frame/line/pixel clocks) – but for the primary board, the S series is still the standard recommendation.
For the ScanImage primary board, the requirement is to sample at least 1.25MHz on all the input channels, and unfortunately they don't have X series options for this except for under USB (e.g. USB-6356 – but this hasn't been sufficiently tested to recommend) or PXI (which requires a PXI chassis) form factors.
Note that if you only need one input channel, then X series boards (635x and 636x models) can be used for the ScanImage primary board.
Please tell your NI rep that we would like to see an X series board offered with 1.25 per channel in a PCIe form factor...then we can begin to phase out the S series. That's what we've been telling our sales rep.