To add a bit more depth, the fees could be graded by how rich the system is, and how much trade it receives. A distant port of call at the tail-end of the line will be glad to see anybody, and would probably have minimal fees. A busy hub, where there's always a queue of ships waiting to get in and docking is at a premium, would probably charge a lot more.
Superhub must have exhorbitant fees then, 'cause I saw my first one the other night, was in the cue to dock, but no-one was docking - probably all arguing with control over the cost
Having said that though, the idea (to add a little immersion) is sound. Integrating it with current economics is less straight forward. Paying for the privilege of jumping the docking cue is a better way of putting 'fined', and charging a percentage of income, I think, is fine. Tying a standard fee to income level sounds fine as well.
Another view - Perhaps there could be a docking fee (perhaps a launch fee) based on value of hold cargo (appended to the same code that recognises that you are carrying illegals). The code would stop a launch if there is not enough credits in the account to pay the launch fee so you have to sell something from your hold to cover it.
Or perhaps in terms of the GST (VAT) idea, this figure is hidden, so all that needs to be stated, on say the commodities screen, is "This includes xxCr of Launch Tax" with no actual change to the trading mechanic. To keep it immersive, perhaps non-luxury items like food, minerals can state 'no tax' and luxuriy items can state '20% tax'. This then becomes a (hopefully) relatively straight forward js calculation oxp.