There's at least one ticket open about hot spares. I *think* I saw another ticket about some issue with FreeBSD that needed to be resolved before this could be fixed but I can't find it right now, I could be mistaken.
You can specify the spare drive(s) when you create a pool, or add them later. I think the only way you can add a hot spare in FreeNAS currently is to create the pool at the command line and specify your spare disks, then export the pool at the command line and import it using the GUI.
Here's a link to the Solaris docs on adding spares: