So I'm not completely sure about the standard 1299 forks but I have just recently gone through my 1199 Panigale R forks. As far as how long it would take probably depends on if you have the right tools for the job. Taking the fork cap off is fairly easy as that should not be torqued very much. Removing the dampening cartridge was initially a challenge as I had to make the correct castle nut tool to unthread the assembly from down inside the inner tube. Fortunately my buddy has a lathe and a mill so I was able to make one. On the OEM Ohlins forks they can unthread in two different places. In my case on one fork it unthreaded at the top and on the other fork in unthreaded at the bottom. Ducati glues both places so it was somewhat of a bitch to get apart. If the NIX 30mm cartridges are a complete replacement for the entire dampening assembly you will want them to unthread at the bottom of the fork. If they unthread at the top then that would suck as the cartridge tube would still be threaded into the bottom of the fork but the dampening rod, valving would come out. If you are just changing the valving then this is fine.
So after all this, my answer would be if you have the right tools, then doing the cartridges are a bit more work than just changing the entire forks all together. Just swapping forks is fairly easy and does not really require any special tools. However after re reading your question I would guess a shop would charge several hours at whatever their shop rate is to change the cartridges. My guess would be about 3 or so.