@Cedar_Z, I do feel your pain, but there are techniques you (and I) can learn to make our lives easier.
There is a probability that they will knock out the user, but I think what's happened over the last couple of months is that people have got a bit smarter with how they use them, so we see self-knockouts a lot less frequently.
For instance, when I first started playing, if I got the nunchucks I'd be swinging them constantly - even if there wasn't another player to hit. When there were other players around I'd swing them while chasing after them. All of this just increased the chances of getting knocked out myself, and I always knocked myself out.
Now, when I get the nunchucks I will only swing them when I'm in a position to get a knockout. In all other cases I'll just walk or run around with them. This drastically reduces the chance of me knocking myself out. I rarely knock myself out with them these days. You just need to a bit more selective with how you use them.
I had the nunchucks in a game last night and was backing another player into a corner on Ichiban, so I could knock them off. I watched the player and they were very still - waiting for the right moment. Even though I was swinging the nunchucks at them they timed a kick perfectly and managed to knock me out and win the round. They managed this because they were a better player than me. So far I've never managed to kick someone swinging nunchucks, but it can be done.
I agree though, even if both of us could consistently kick someone with nunchucks, it would still be difficult and risky to do so on Gator Valley or Broken Arrow. It's worth noting that every weapon has a vulnerability. The nunchucks are especially vulnerable to ranged weapons like the crossbows. If I don't have those I will often use the roll to avoid being cracked in the face by them. The roll is a bit safer on Broken Arrow than the kick, and it gives you some breathing room and time for another weapon to spawn (hopefully the crossbow or 1000T hammer).