I think it is so expensive right now because if you go straight to the black market to sell legal goods that would avoid tariffs, so the authorities need another way to drain your money so the black market is not OP.
I think maybe inspection frequency and severity of fees incurred should be based (more? is it a factor at all right now?) heavily on system stability and smuggling activity.
If a system is more stable than not and there's little or no smuggling being done, these legalized shakedowns should be much, much rarer, and the toll should be absolutely tiny compared to what it is right now.
Legal traders already have to face enormous tariffs, after all.
Hell, maybe there should be a reputation stat that ties your history of legal trading and helping out with shortages in each system with your faction standing, and should count for or against you with this kind of stuff.
"Hey, I scanned your cargo and it all looks good. We usually charge for this kind of thing, but you're a dear friend to the Hegemony, and the books also say you rescued planet A and B from starvation with your onion shipments! My wife lives on planet B! My god, someone give this man a medal."