If you used JBOD you have to use the appropriate command line options for your hardware. You'll have to read up on using 3ware with smartctl to get the SMART data.
If you used a bunch of single disk arrays(a lot of people do this by default) then based on my experience with a 3ware 24 port controller(forgot the exact model) you won't be able to query SMART data at all. This is not a good configuration at all since reading SMART data can clue you in on a failing(or failed) hard disk.
While 3ware isn't an ideal card for FreeNAS, if you use JBOD and can navigate the command line and interpret the SMART data yourself it can make a very trustworthy configuration.