*poofs*
To correct some misinformation:
-Shinobi and Samurai weren't exactly enemies. While one may frown on the others methods, they would only be enemies depending on their affiliation. Many Ronin (leaderless) Samurai became shinobi. Most of that "Bushido" code came when Samurai became more of a political-role, rather than martial. If it was always there, why are most of the beginning of forms of iaido usually start while you're seated, with blade sheathed? And taking on several opponents?
-The Ninjato is a fictitious sword. Most of the time the shinobi would either take katana's off dead samurai, or have a shorter blade (wakazashi) in a katana saya. This way, when drawn, the opponent would anticipate a longer blade, and would be "cut short." The most likely "prototype" of a ninjato was just a poorly made katana by lone blacksmiths, or just "machette" type utility knives.
-Daisho (set) was any katana/wakazashi. It was EXTREMELY rare for you to get a matching set, and VERY expensive. A mark of either being very wealthy or affiliated with a very rich lord.
-The Katana was honestly more of a sidearm, much like the pistol is today. The "assault rifle" of the time would be a naginata, or other pole arm that would reach the enemy before he got to you. The reason swords are most likely associated with warriors, is because they're convenient to carry, much like a pistol. So warriors not engaged in war, would carry their swords as a side arm (and also to mark them in the warrior caste, just associating the sword with battle.)
-The wakazashi I do not believe was the blade used in sepukku, it would most likely be the tanto.
-The Wakazashi was used for areas in which the katana would be cumbersome to wield, like small hallways. Also, the famous Miyamoto Musashi made the dual-wielding style quite famous, using the wakazashi much like a main gauche.
*unpoofs*