This is actually a common method in such implements as UPS units where two 12V batteries are connected in series. The fuse acts like the jumper that connects the two batteries together, and guarantees that just about no matter what circumstances are encountered (except a puncture of the cover over the fuse), the circuit will open and protect the wiring.
Only thing I would add to this is having a
master link in addition to your individual fuses, at just a slightly lower rating than the collective of the individuals. For example:
+++++++++++ ~ +++ to bus
6v 6v Master
- -
| |
fuse fuse
| |
+ +
6v 6v
---------------------------- to bus
If you have 6 sets, each fused at 20A (for example), use a 100A master link.
This prevents an expensive and irritating blow-fest (as sparweb pointed out) amongst your individuals should something crazy happen downstream of the master link. One fuse (particularly as currents go up) is cheaper than 6, and certainly simpler to replace!
Steve