Yes, FreeNAS can access SMART data. You'll want to turn on that service in FreeNAS, make sure you've set up an email address for alerts, and schedule SMART self-tests regularly.
I did read the doc recommending SMART be disabled if HDD is connected to a RAID card. So not sure does that applies to my IBM M1015 flashed to LSI 9220-8I IT.
I think an IBM M1015 flashed to IT is pretty much golden. You can proceed with everything, including SMART, as if you were direct connected to the mobo.