Where to fuse high voltage batteries connected in series?
If the purpose of these modules is to be 'modular', that is they can be removed, replaced, handled separately, then one fuse per module, to protect each module, would seem to be a good investment.

If the load wiring requires tighter protection than the modules do, then put a further fuse in series with the wiring. The normal expected place for such a fuse would be next to a contactor, just to avoid surprising people.

While there is no difference between the three locations as far as breaking the current is concerned, the second option does result in lower voltages remaining after a fault opens the fuse. 48v is still rated 'touch safe' whereas 96v is not. Whether your post-fault fault-finding instructions would ever allow you to make safe use of that small advantage is another matter.