It wouldn't simply be that all trading is effectively the same, but instead that trading interacts with far more variables and the abstracted NPC trading would soften most of the extreme circumstances. Trading effectively would be about finding situations wherein the NPC trade fleets are either unable or unwilling to meet demands. This could be if key systems have fallen into anarchy (which would drastically affect systems that don't have significantly militarised trade fleets), it could be that the supply and demand are on opposite sides of a superpower divide, it could simply be that players are willing to trade over much longer distances than normal NPC fleets.
The first problem with "longer distances" is that the bubble is largely homogenous - it's not that all the extraction systems are at one end and all the refineries at the other - so pretty much every system has several nearby sources of almost all trade goods.
The second problem with "longer distances" is that with Fleet Carriers (or even a half-decent ship) nowhere in the bubble is a long distance from anywhere else in the bubble for a player. With extremely slow travel - Elite I style - then distance could start to be meaningful even on a regional level. But that's not going to happen.
Effectively, short-distance high-profit routes should be rare and typically have some kind of problem with them such that players would have to identify what kind of edge they have over local trade fleets in order to turn a tidy profit. If there's a clean, quick and safe way to earn lots of credits without any major issues, then the NPC trade fleets would burn it out within hours.
Okay, but how "rare" is "rare"? There are 20,000 inhabited systems in the bubble, most of which have somewhere between 20 and 50 other inhabited systems within a single 20LY jump. That's, say, 350,000 short-range trade routes, 150ish common commodities, so about 50 million possibilities, and it requires trivial "big data" analysis to find the best one.
Getting "rare" to "less than one in fifty million" but not "zero" on a system this noisy is basically impossible.
Courier, passenger and data delivery missions would have the same limitations - if it can be done easily by a faction's fleets or via general commodity markets, why would they need to pay someone way over the odds to do it?
Sure. Now given that everywhere in the bubble is essentially 15 minutes away from everywhere else in the bubble, and even the tiniest faction demonstrably has hundreds of ships and pilots at its call, why would factions hire independent pilots at all, for anything? Realism has its place but if the conclusion is "why are players even able to make a living, they should be toiling away in the Lepidolite mines like the rest of the NPCs" that's not really the point of Elite.
Disrupting a single system would have wider effects on the regional economy
Even in Colonia with it's tiny economy I can't think of a single system you could disrupt that would make any significant difference to regional trade.
demolishing a particular factions trade fleets would impact their ability to resupply themselves
Yes, but you'd be hostile to them so you couldn't take advantage of that yourself.
This is also basically there already - that sort of negative action (if the dominant BGS force) is likely to generate a state such as Infrastructure Failure, Terrorism, Blight, etc. which massively but temporarily increases profits on certain trade goods.
The pirate issue I feel is far deeper reaching than simply the bounty values ascribed to pirates and the other direct economics behind them. Pirates in this game are dumb. As in, their density collapses galaxies, their monumental stupidity is visible from Andromeda and their foolishness has every philosopher to exist in every species spinning at 7200 RPM in their graves.
Okay, sure, that's true. So the pirates act like economically rational agents and sell their ships to live a life of luxury on a private tropical island with all the Lavian Brandy they can drink, the bounty hunting profession collapses because no-one does anything illegal, and we don't need to worry about balancing either
Elite-series piracy has never been even close to economically sensible, unless you assume that the value of the goods not reaching their intended destination is the real goal, and they're all funded more to disrupt rather than steal shipping (which would explain why most of the half-decent ones don't even pretend to be here to steal your cargo).
(Obviously the idea that it might be more rational to blow up a trader than try to rob them would go down very poorly with the "griefers!!" crowd, but the economic argument I think is pretty sound and has plenty of historical precedent. WW2 submarines weren't out there with the Jolly Roger
robbing merchant convoys.)
Other services might be quite difficult to work with, particularly exploration. Exploration definitely needs some kind of diminishing returns based on how many people have already explored an object as a softer alternative to the "first discovered" bonus, probably further scaled by how far that object is from human space; this would prevent exploits like the "road to riches" as a large number of players performing the same route would rapidly devalue it and so would naturally encourage explorers to wander off the beaten path. It basically comes down to applying logic behind the value of discoveries and how much Universal Cartographics would pay for the information rather than just each stellar object having a fixed value.
It stops people getting lots of money without even leaving the bubble, but I can jump 100LY from Colonia and get "first mapped" at a couple of million a time on a basically unlimited number of terraformable HMCs. If I jump 200LY I'll start getting WWs, AWs and ELWs too. If I head a few thousand LY corewards I could go for days without ever seeing another discovery tag. The supply of newly-discovered systems containing nominally valuable worlds is for all practical purposes unlimited, and travel speeds make them all to within a basic approximation "nearby" for the optimising player. What limits the demand (without saying "look, we already know about 100,000 ELWs, even your first discoveries are basically worthless" as a blanket policy)?