Crusader Kings makes the mechanical effects of decisions explicit when you are presented with a list of choices. However, decisions are often non-deterministic: usually they will say things like 50% chance of surviving and gaining a good trait, 50% chance of dying.
You might have each choice tell the player what mechanical effect they are intended to have on the game. However, if you want to make decisions risky and still let the player have full awareness of negative consequences, you could also list the chances of negative events occurring. In addition, you could also hide potential negative events, and indicate only that there is a large or small chance of an unspecified negative random event occurring as a side-effect of a decision.
You could also have the personalities of the current guild or faction leaders add further additional effects; for example, siding with the Spacer Guild over the Trade Federation might decrease the cost of freighters but also decrease trade income. At the same time, the Spacer Guild members simulated by the game might each gain loyalty depending on each individual's personal view of the emperor, and the Trade Federations might similarly lose loyalty on a case-by-case basis. A cowardly Trade Federation leader might even gain loyalty in an attempt to further appease the emperor. On the other hand, putting a vengeful leader on the receiving end of a negative decision might set off a new storyline where she seeks revenge.
===
One idea for courtiers might be to set up Ministries (Trade, propaganda, military, navy, personnel, etc) within the imperial court. You would assign a leader of each ministry, and assign courtiers to each as underlings, and the courtiers would grant bonuses to that segment of the empire, add bonuses in relevant decisions, and potentially foment intrigue/storylines as they attempt to rise in their ministry's internal hierarchies. You might have ranks for the courtiers in each ministry so that the courtiers are constantly jockeying for position. Courtiers at the top might give higher percentages of their stats as bonuses, while courtiers at the bottom contribute almost nothing. You might even have courtiers who are bad at their jobs and decrease productivity, but must be left in place for political reasons.