It appears that the Japan Armored Battle League is actually about to test this hypothesis. Next week, in fact:
Japan Times
JABL Homepage for ticket purchases
Man, I wish I was still in Japan.
I like the fact that it's three full teams of knights and samurai, not just a one-on-one match. More data points :)
They've also specified all of the rules beforehand, but they're only available in Japanese. Basically, what they've outlined at the moment has to do with armor weights and weapon dimensions, and no blows to the groin.
Ok, samurai have their kanabo, I will give the battle results now:
Knight 55
Samurai 45
(Reasoning. The better armor will may deflect a blow, but the samurai is more mobile. The knight could raise his visor after closing for a better field of view (but this gives a target if the samurai wished to switch from his kanabo to his katana, but probably wouldn't, one target area is easy to defend. The kanabo was difficult to use, but would break bones (through the armor) and shatter shields; it was hard to recover from a miss giving a well trained knight the opening. Training is about equal. Bushido prohibits striking the legs, while the knight has no offsetting restriction and may be the deciding factor. In some instances the samurai's bow would end it before it began, but the knights shield, armor, and helm lessens the number of successes).