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I see a few different questions here so I'll address them seperately:
Following up on point #1: You should be fine with a regular-sized SATA drive, since mSATA, M.2 SATA, and SATA 3 all have the same data rate specification. Big thing to keep in mind is the trace length requirements outlined in the System Design manual (Table 15, page 32).
One more quick question. Valid power supply range for sbRIO-9609 is 9V to 30V. Just want to double check that a 12V power supply with about 10A ~ 15A current should be fine to run the system, including one SATA SSD.
I can't speak to the SSD itself, but the 9609 has a max power draw of 28W. So 12V @ 10-15A should leave plenty of headroom for the drive.
If your wiring is not matched to the right impedance, you may have errors on low level, and you're not going to get much notice on such issue, the system will auto retry to get right data.
You may take a look at the S.M.A.R.T. data in 9609, maybe there will be some low level information on SATA IF.