If the cover is not on (or not seated properly) the OS will unmount the internal SD card (if it's not currently in use - if it's in use it will instead display a warning). If the cover wasn't on when the N800 is booted it won't mount the SD card until the cover is placed back on.

On the inside of the battery cover there is a small square just below the top latch - a small magnet should be glued into that square, which the N800 uses to determine if the cover is in place. When the cover is closed the magnet sits just to the top right of the SD card (there is a small hole in the metal plating where the magnet sits). If the magnet is missing from the cover it will of course not detect the cover; if you can place another magnet over the opening and the OS mounts the internal card the problem is with the cover. I was able to get the N800 to mount the internal card simply by placing a magnetic probe from my electronics tool kit over the opening in the metal casing. If the magnet is weak for some reason (or fell out) simply replacing it with another will probably do the trick. Otherwise it might be a bigger problem with the hardware.