i usually recommend a bottom up diagnostic process, and also clarification on what you mean by "none seem to show up on FreeNAS" because that could mean different things (not showing up in the OS? now showing up in FreeNAS UI? you have an existing pool on those drives and you don't see the ZFS pool in FreeNAS?)
1. start with the hardware. when you power on the server, do you see the heartbeat LED on the LSI SAS2008 card blinking about once per second? if not, your card's firmware isn't running for some reason. fix this issue before proceeding.
2. if your LSI card has the BIOS ROM installed, during POST, enter the BIOS ROM program when prompted. Usually requires you to press "ctrl + c" or something like that. in the BIOS ROM program, find "SAS Topology" and enter that screen. You should now see a list of all connected storage devices. Do you see the HDDs there? if not, you have something else wrong, perhaps wrong type of cable? poorly connected cable? damage to the LSI card? (inspect the capacitors on the SAS data lanes near the SFF-8087 ports)
If your card has a heartbeat, and the drives show up in the BIOS ROM "SAS topology", then it's pretty safe to say your issue is not a hardware issue. Then, the next step is to troubleshoot within the OS (FreeNAS). Personally, I like to do stuff on the command line since this allows me to distinguish a problem being a OS-level problem or a GUI-level problem. So, for much of the following, open up a shell terminal (via console, SSH, or within the GUI). BTW, i'm actually much more of a Linux guy (sorry, don't hate me), so my BSD-isms may be out of date or wrong / if you spot an error please tell me so i can correct it.:
3. make sure the LSI controller is detected within FreeNAS. from a root level shell, run:
# pciconf -lv
And see if you find your LSI controller. If not, then maybe your problem is that passthrough isn't working or something else; troubleshoot this further. If you do see the LSI controller, go to step 4.
4. make sure all the HDDs connected to the LSI controller are seen at the OS level. from a root shell, run:
# camcontrol devlist
if you don't see your HDDs here, but did in step #2, then there might be a OS-level / driver problem going on here... troubleshoot this further. If you do see your HDDs listed, then OS sees the HDDs.
If everything is okay up to step 4, then the next steps depend on your clarification of what you mean by "none seem to show up on FreeNAS".
hope that gives you a path to diagnose the issue... good luck.