It will mess up with the Katana sound for sure, the thing is the kemper kone is engineered to work closer to the celestion F12-X200 for what I can see in the frequency responses some people have taken out:
Like this one
So what happens is that the cone has a higher output in the highs and some mids than a conventional speaker, so post kemper magic (EQ) the frequencies are eq´ed out and get the cone to sound really close to the real deal. The magic here is the kone is designed to have high spl and move more air than a conventional flat response speaker.
So what you will hear without the kemper eq, is a very very fizzy output from your katana channels, and I doubt you will be able to eq that out and make your sound as before. I would not recommend it. If you already have the katana, keep it as it is, if you want the kone magic but keep the nice katana tones, there are 2 ways, profile all your favorite katana tones and change the speaker for a kone, so you always use the kemper as preamp, or make a kone cabinet (get one kemper kabinet) and modify your katana so you can connect the output to the new cab (the 100 mkii has no speaker output ports sadly). I would rather keep the katana as it is, and buy the kabinet and a cheap power amp to run it (BAM200 or Powerstage 170/200)