Simple and compact Over-Voltage protection with fuse and resistor
Will this circuit protect against such a device? How effective is this protection?

Not at all.

The fuse will blow slower than the traces.
Why would anyone decide to try to blow the power rail (which is definitely easier to protect) instead of the data lines
a fuse blows when a critical current already flows. You can't really have that.
You're not even attempting to fuse the shield
This is a vain attempt – if your attacker has arbitrary much energy at their disposal, there's simply nothing you can do. Think about what happens when someone takes a high-powered electric arc welder to your computer. Will your fuse help? Modern batteries contain huge amounts of energy.
Honestly, what are you even protecting against. As 90% of bad computer security things, this was consideration done without proper threat modelling. If someone wants to incapitate your USB host device, a hammer, a drill, a sharp screwdriver, chewing gum, half a glass of water, a stone, urine will work too, unless you fully encapsulate your device and make the USB plug unavailable. If the USB plug is &quot;optional&quot; functionality, without which you want your system to still function, then don't make it available to begin with.