After looking over the SAM 460 mobo manual, it does indeed have a Hard Disk activity 2 pin jumper, as expected.
Block J29 - 1-2
As for whatever case they are supplying with a prebuilt machine, I can't vouch for that.
If there's a PC case without a HD LED, I've never seen it.
I recommend contacting the vendor you are considering dealing with just to make sure - for a small scene, us Amiga guys do have excellent retail support.