I'm afraid I have to question your notion of Nobility in a historical sense.
Nobles were frequently fractious and gave their King much anguish. The King could not simply have a Noble punted because many of them held noble authority from times before there was a King (the King position having come out of groupings of higher ranking leaders of small regions deciding one could be the head honcho). The King could enfeoff subordinates in his lands, but the lands of the other nobles WERE NOT the King's lands. The nobles did offer fealty to the King (in return for his responsibilities to them) but they did not waive their own rights. They could enfeoff people under them without the King's permission (on their lands, held from times before records).
Scottish and English Kings certainly had to deal with these realities. Now, the King held a lot of land and any new land he conquered extended his powers and the occasional traitor lost their lands (or those on the losing side of a war with the Crown) but there were some ancient claims on land the Kings had no hand on quite late (maybe still do, but I doubt that, but definitely out through the 14th or 15th century at least).
So, it depends a little on how you see nobles and which game area. And since the *vast majority* of what came later about Nobles (in post CT and definitely post early-CT eras) may not apply to the less defined, less restricted early game setting.
Remember, we didn't see all the details of the expansion of the Imperium, but you can be sure that the Emperor was granted some rope by his supporters (admirals and other people of importance) but they sure would not have given up all of their rights and prerogatives to him. He'd have started out with a few modest powers, but the Dukes and Counts had prerogatives too. As things expanded, he would have minted more nobles through conquest and they may have held land through the Emperor but even then, the older/more powerful families of the Core and elder colonies would certainly have also expanded their holdings.
Over the long haul, the trend may have turned nobility into a job that happens to have particular respects and perks, but that's NOT what nobility is at its core - control of territory where said control is essentially unabridged. There's likely much less of that by 1000 Imperial reckoning, maybe even a few hundred years sooner, but you can bet that even in the 3I, there are still old line nobility that retain true noble powers, rather than simply getting an estate and an honorific as a nice retirement benefit for being a bureaucrat.
The one thing I do see becoming more likely as the Imperium aged is a theoretical shift from a Rule of Men to Rule of Law (more structure, more order, more bureaucracy) but with the powerful old line families and the corporate ties they have (and the nouveau nobles made by conquest more tied to the Emperor), as well as the sheer bulk of the Imperium, Rule of Law just becomes administratively necessary.
That said, there are families who have been knife fighting and engaging in various corrupt manipulations for possibly 2000 years by 1000 Imperial. That's a long time. And they are probably very good at this sort of work. So that's why I called it a theoretical shift - money and old nobility connections trump the Rule of Law most of the time (but as the issue only gets notice a very small % of the time, that supremacy of money and nobility is largely missed by many of the little people in the Imperium who believe that it is a Rule of Law place.
Just don't get on the bad side of someone with real power from before there was an Imperium
This reminds me of Dune's houses of the Landsraad (sp?).
TomB