Well Yes and No.
Now you’ll have to forgive me as I don’t have a Netapp disk shelf nor have I used one (although have used other OEM boxes in varying setups). I have only quickly skimmed the manuals to see if there is a way to do what you are doing without drastically changing the way you’re doing it.
No, you can’t do this. Currently you’re running the Disk Shelf in what would be called a DAS (Direct Attach Storage). This means that the storage system you’re using it on is the one handling storage and committing stuff to that storage.
The two controllers (although independent) work together to form multiple paths to the disks and they can’t be configured (as far as I am aware) to separate the chassis, eg disks 0-11 to controller A and 12-23 to controller B.
(Side note: Dell MD1000 (and family) can do this)
In the scenario where I say Yes, you require additional hardware. You need to add a controller gateway (a gate keeper of the storage) and essentially build a SAN.
NetApp have a bit of kit for this, however it’s over kill unless you can get one for cheap.
In this case you’d end up using the ACP ports (the network ports on the controllers) as well to allow the shelf controllers and gateway to correctly identify paths and failures in said paths.
You’d be best to just load the additional disks into the chassis, configure them in FreeNAS and then just share them out to the other machines that require them (whether that be through iSCSI or with a file system using CIFS/NFS etc).