In his two sword style, perhaps, but he actually only used that fairly rarely as I recall.
I'm grasping for the translation off hand, but I recall it being Two Heavens style. In his Book of Five Rings, he speaks of it being a waste of your hands (essentially) to use both of them for one sword, likening it to an unnatural movement for the body.
Speaking from first hand experience, even with wrist strengthening techniques and training; using a katana or similar weapon your movement is noticeably harder to control and less refined, not to mention a greater lack of strength and sturdiness. But japanese sword fighting is more similar to fencing than other more direct styles, in that you don't block hard you parry most blows that you otherwise could not dodge.
So rules wise, I think the -2 for wielding a two handed weapon one handed is apt, but I honestly think that should apply to any weapon that is classed as a sword. Knives are a different case because they're used in conjunction with grappling and don't rely on a wide swing radius and arm strength, so they need to be used one handed.