In this example, the Hida Bushi will most likely be terrible at seduction because it runs off Awareness, which he has no use for, while Intimidation runs off Willpower. If our Hida Bushi happens to also have high Awareness for some reason, I see no problem with him being good at seduction. I likewise see no problem with a Bayushi being good at Intimidation if he happens to have high Willpower; blackmail is an iconic Scorpion technique, and it is by definition a form of intimidation. Fear in both general and specific forms is integral to how the Scorpion get things done.
I'm also not clear on what "a samurai should never rely on Intimidation or Temptation to do his duty" has to do with whether it's better that they be separate skills or categories of other skills.
You would have to define what's terrible. I'll take the Meta for Hida O-Ushi in the Way of the Crab as an example. In her meta, she's a rank 3 Hida Bushi with an Awareness of 3, Willpower of 5 and Intimidation of 5. This would mean that she would have 10k5 in Intimidation and 3k3 (and no 10s explode) in seduction. If we fuse Intimidation with seduction, her seduction would become 8k3 (10s explode), which isn't terrible at all. Yes, she's the same in her intimidation but she's now a competent in temptation, which doesn't fit her at all.
Ought Hida O-Ushi be incompetent at seduction? Or is she simply not interested in doing it?
As for Blackmailing, yes, it's their iconic technique and they are using it using Courtier (Manipulation or Gossip). It would be pointless for them to rely on Intimidation in addition, because it would expose their technique too easily. Just take a look at the very first technique of the Bayushi Courtier: "You gain a Free Raise when using the Courtier skill to spread gossip, and need not Raise in order to conceal that you are the source of that gossip." it's pretty clear to me that the Scorpion don't rely on intimidation for their blackmailing technique.
Given that we are talking about blackmail, I have no idea why you brought up gossip. They're practically polar opposites; blackmail is, among other things, a promise not to gossip (if the victim co-operates), and a threat that there will be gossip (if they don't). If a Scorpion approaches too and says "I know all about your littles games with the funds your lord entrusted you with, and if you don't do X for me, very shortly your lord will know too", that's Intimidation.
As for the "I'm also not clear on what 'a samurai should never rely on Intimidation or Temptation to do his duty' has to do with whether it's better that they be separate skills or categories of other skills." it was toward the idea of the elimination of the Low Skill, not about fusing them or not. As an answer to "One of the things which is trying to be done by the elimination of the Low skill group/tag is the idea of dishonourable practices being possible with all sorts of skills."
And? I'm still not seeing the connection. In what way does changing Intimidation from its own skill to a dishonourable Emphasis of another skill change "whether a samurai should rely on Intimidation or Temptation to do this duty"?