"Well I learned from a Karate instructor that you need several sustaned hits to imobilize some one with nunchucks - he only needs one lucky stab/slice."
Sounds like a Kempo instructor wuss

(no offense to my Kempo comrades

).
You can easily immobolize someone with a single strike if you are using the right type of nunchucks and know what you are doing. A couple quick and relatively easy ones, thrust to the throat or to the outer corners of the eye socket(on the edge, will fracture a decent portion of the skull). For type, 12"-16" octagon chain/bearing, you don't want rounded in combat nor do you want rope/swivel, they don't offer enough speed through all rotations. Don't try and "practice" this unless you know WTF you are doing, hitting someone in the throat can easily kill them, never do this unless you are in a life threatening situation, same with the eye socket though it is rarely fatal it can cause severe permanent damage.
"Assuming someone has a pretty good efficiency with nunchucks against someone just messing around with a kitchen knife, I would still want to be the one with the nunchucks. But yes it might be a different story against someone who knows how to wield a knife."
I'll take the chucks, anytime. Knives are easily turned against someone, particularly with chucks. Remember to use swing/wrap on any thrusts(defensive for you, offensive for knife bearer) and the knife is easily used to your advantage. Swords on the other hand.....
Good practice for that is to have someone with some cheap makeshift spears try to stab you over and over. When you get the hang of down you will be either breaking the spear everytime(broken arm) or flipping the spear out of your "opponents" hand which results in the muscles in the arm being forced to relax and the knife dropping to the ground, leaving only you armed.
For knife throwing/defense, have someone throw softballs at you over and over and practice swatting them away at first and then using thrusts to knock them back. When you get the hang of that down, move to baseballs and then golf balls.
If two properly trained individuals clash one with chucks the other with a knife, odds are four to one against the knife bearer, they would be even more slanted except for the lucky slice part(which can be painful even with practice gear

).
Oh yeah, I own a couple pairs(or more) of chucks and a Ruger 10/22. Only ever use it for target shooting, and haven't fired it in a few years(mainly because the gun is stored ~50miles away, no child house, and I don't have a lot of spare time).