You mean having a fuse within 18" of battery-a(in engine bay) and another within 18" of battery-b located in the trunk?
OR
You mean having one on both the pos. and neg. wire?
Fuse is there to protect the wire. If for some reason there is a power surge(spike) that is in excess of the allowed wattage of the wire, the fuse will pop and cut off any power from flowing. While not having a fuse will allow the surge to continue thus heating the wire and the surrounding area and eventually starting a fire if the heat is hot enough...
what can happen is the battery on the unfused end overloads the wire and you need to buy a new wire. chances of it happening slim but thats what "can" happen.