On Honour and the Scorpion
So, I figured I should probably sit down and actually outline how Honour is going to work in this Quest, which is an extension of my own views on the topic. Note that this is kind of homebrew to a certain extent, because the rules can never hope to really encompass an entire philosophy of life followed by hundreds of thousands of people in various divergent ways.
In a mechanical sense, your Honour score is a numerical value from 0-10, with 0 being 'Honourless Dog' and 10 being 'Strength of a Thousand Ancestors'. Naoto currently has an Honour score of 4.2, which is described as 'What is Expected'.
Gains and losses in Honour are awarded in 'Points', each of which is worth 0.1 Honour on the overall scale. Different acts and behaviours give or cost you different amounts of Honour points. Notably, there is an increasing gradient in play - at higher levels of Honour, positive actions award fewer points and negative ones cost more.
Mechanically, the primary benefit of Honour is that you can add your score to any rolls made to resist fear, intimidation or temptation. It is also your one source of 'rerolls' - if you fail a roll, you may choose to use your Honour rank as rolled and kept dice on a reroll in order to try and succeed despite the initial failure. It can also be perceived to a certain degree by other samurai (generally by succeeding on a TN 30 test of Lore: Bushido/Awareness, though I would lower the target number if you observe the target at moments of moral choice).
What is Honour?
Honour is, essentially, your adherence to a personal code of conduct, and the strength you draw from that. It is the foundation which supports and reinforces your overall character, the integrity and principles that make you who you are. In many ways it represents your efforts to realize your ideal self image, and be the person that you want to be.
In Rokugan, the default set of principles for a samurai is the Code of Bushido, though others (such as the Code of the Wasp or the Way of Shourido) do exist. A thousand years of social convention and reinforcement have established 'adhering to Bushido' as being all but indistinguishable from 'being a good person' for the samurai, and even those who do not follow all of its tenants do not usually disagree with them - the Scorpion still think of themselves as villains for their constant violation of honour, they simply believe that such is a necessary sacrifice.
So far, Naoto is receiving numerous increases in Honour because he has been acting according to a strong set of personal beliefs. He is loyal to his clan, he shows kindness to those below him, and he is civil even to those who think themselves his enemy. These contribute to his self image and inform his choices - you will note, for example, that several times an update has made mention of Naoto being tempted by or considering a course of action but deciding against it because it conflicts with his duty. The more he resists such temptation, the easier it becomes, represented by adding his Honour rank to resisting Temptation rolls.
Why do the Scorpion distrust Honour?
The Scorpion and the Crab are the two Clans who start with low Honour scores - generally 2.5 for their Bushi and Courtiers. This not because they are bad people (though individual members of each Clan can be), it is because they are pragmatists. The Crab have no time for pretty speeches or shining ideals on the Wall, and the Scorpion define themselves as being willing to dirty their hands with the unpleasant but necessary tasks to keep the Empire running.
The Scorpion in particular disdain those with a rigidly inflexible moral code because they believe it will constrain them and prevent them from following or even considering certain courses of actions. In the Courts, playing dirty often works, and the Clan of Secrets has no patience for those who would shun a viable strategy due to their own squeamishness. This is where their concept of Junshin comes from, and why they instinctively distrust those who think of themselves as highly principled. Bayushi Yojiro is a fine example, because when the Clan ordered him to destroy a man on their orders despite the fact that said man had done nothing wrong, he hesitated. The fact that he went through with it afterwards means relatively little.
That said, the Scorpion are also the Clan of Loyalty. They hold to the virtue of duty/loyalty with an almost maniacal fervour, and it informs the basic moral code that all true Scorpion abide by. If Naoto can demonstrate that his personal code and increasingly high Honour score supports his loyalty rather than conflicting with it, the Scorpion are likely to embrace and support him just as much or even more than any other Clan would.
It is a narrow road to walk and one easy to falter on, but if you can pull it off you'll earn the respect and admiration of all the Clans, not just your own.