In the end yes the fuse will protect the Leaf's DC-DC, but what is really protecting it is the battery up front, the lines running to the back and then primarily the rear battery. All these will reduce surge on the DC-DC converter. I honestly doubt that sub will pull more than 100w continuous unless your pumping white noise through it, sure it might surge to close to 1000w but in short bursts for milliseconds.
One way to think of it is the main DC-DC converter is a supply or hose of running water (water being power) and the first battery is a tank and the "hose" leading to the second battery as another tank. All the main DC-DC has to do is re-fill those tanks, the instant surge will be pulled from the closest battery or "tank" to the amp and will then slowly refill.
I am not sure what size you will run from the front to the back, but even at 4 gauge, unless you dead short it (that's what the fuse is for) you shouldn't hurt the car. Just remember to leave the car on, if you manage to run the 12v dead you won't be able to restart it.
3 kw solar pv - XW6048 - eight L16's
4 ton GSHP - 1 ton ASHP
2003 VW TDI 200k miles - 52 mpg lifetime
EVSE level 2 - Clipper Creek HSC-40
2013 S model with QC package Mar of 2013
lost first bar @ 72k
@90k miles - 54.71Ahr - 83.64SOH - 78.44Hx - 237GID