I own an Apple iMac and I would to directly connect it to a NAS using the Thunderbolt port. As far as I know, FreeNAS does not support this. Do you know of other open source projects that can do this?
A Network Attached Storage (NAS) device is normally used as a storage device that shares data over the network. What you are trying to achieve is possible in theory, but it is very uncommon and may therefore be hard to get working.
First of all, support for Thunderbolt is quite low in open source operating systems. As you figured out, FreeBSD has no support for it and Linux only supports it starting from kernel 3.17.
Secondly, since NAS distributions usually expect you to connect to the NAS as a network device, you might run into trouble if you try to work around this. Personally, I use a NAS to make backups and I'd like to keep these as safe as possible and I avoid workarounds.
I'd advise you to build a proper NAS and simply connect to it using gigabit ethernet, which is already pretty fast.
EDIT: there's no distribution that supports what your trying to do by default. This doesn't mean it can't be done. I'd start with Open Media Vault and try to install Linux kernel 3.17, possibly from the Jessie repository (OMV is on Squeeze, I think).