2. Because they're armed. Because broken men behave in particular ways. Simpering, avoiding eye contact with their master. Lack of confidence. No backtalk. No signs of harsh physical abuse that would be required for such strong-willed individuals to be broken. Scars, bruises, burns, sheered fingers. All the little cruelties that would be expected from a Dark Jedi intending to become a Sith. That sort of thing isn't required for non-force sensitives.
3a. Individual interest outweighs collective interest in Sith philosophy. Extra converts are not worth being overthown, and that's not how the recruitment process works in the academy anyway. They only pick one student in the end. I agree there are other reasons for Bastila not wanting to go on Korriban, but they're not the primary reason. In that regard for risk of temptation, Juhani shouldn't be there either.
3b. There is no way to anticipate that ahead of time. There is no justification for the PC to take that risk when infiltration is the goal.
4. Related to point 2. Murder is fine among the Sith, however, each of them is desperately trying not to be murdered. Uthar's goal is to remain master. His secondary goal is to replace Yuthura because she's too ambitious. His third is to train new Sith. Yuthura wants to bring in a hopeful with Force Sensitive slaves? Cool, he can leave them in his locker until school's out.
5. I'd have just confined all three to the ship. There's a risk of high ranking Sith being present in Dreshdae and I'd want as few questions coming my way as possible. One unknown fallen Jedi coming to Korriban is nothing out of the ordinary, three travelling together at once stands out like a sore thumb.
Calo would not have necessarily divulged info of the Ebon Hawk to Malak. He's a famous bounty hunter with a reputation to uphold so he would not want the Sith beating him to the punch. It was also personal matter to him at that point. No one had ever escaped him before. The Ebon Hawk is recognized in Dreshdae only by Czerka employees and smugglers, not the Sith.