Question is why are vassals so uniquely terrible at managing their economy, or if they all are why are they still this broken.
Hegemony Federations give the president all the same power as a vassal overlord, without applying penalties and the perks of the Hegemony are a cherry on top.
I'll focus on these two since they are easier to answer
All AI are terrible at managing their economy, and they are still very broken to this day. Though Paradox Devs are looking to change this as time goes on and have made improvements. There is an AI change that I think is being tacked onto the upcoming 3.3 Unity Rework that should help fix the problem even more.
To compound why the AI are terrible at managing economy, it is basically due to programming. The AI will make constant checks on jobs for open slots, often this results in AI moving a lot of pops around to one job and over-compensating: thus, leaving other jobs either low or empty...which then snowballs. The AI move back to those jobs that just opened up due to them moving and it kind of creates a loop effect. This also causes a metric ton of lag in the late game.
The AI also seem to enjoy hell expansion...which has its own problems that need to be touched on and I have no idea where to even start there.
Generally, if you have a Vassal, it is best to integrate them asap...or just release them to be free and fight for themselves.
As for the Hegemony thing...since that is a Federation system, which functions very differently compared to the Vassal system, it isn't exactly a fair comparison.
Even if the Hegemon Federation Leader has the same benefits of being a Vassal Overlord without having vassals and has the bonuses of being in a Hegemon...that is a completely separate issue that needs to be tackled.