No, the pads will not rub. I proved that on my Ninja. My yz 250 fell on my Ninja. Jealousy, I suspect. The right front rotor was bent. I did straighten it, but ended up ordering zx6 rotors. Just like our situation here, the zx6 rotor was 1mm more thick. The zx6 rotors were 6mm, the oem Ninja 1000 were 5mm.
I spread the pads out when I removed the caliper. This makes it easier to slide the wheel back in. I pumped them back up, and there was no extra drag. The fluid level in the m/c was higher, but thats it. Just like the c14, the 4 pistons on each side are able to slide back into their bore an extra .5mm.
I'd imagine the zx14 rotors are the 6mm spec as well??? I'll have to take my micrometer over to the shop and check.