Look, the price of things in the real world is based on what people are willing to pay and what sellers are willing to sell for. That's a fact. ( unless you live somewhere where prices are forcibly fixed or dictated. )
If I try to sell apples for $400 each, you will simply find another seller who is offering a more reasonable price. Likewise, sellers have a limit on how much of a resource that can sell. Npcs don't. If you were to sell apples well below fair price, you would deplete your supply and not profit - possibly take a loss.
In my example with swords, I demonstrated the effects of having an NPC offer a fixed price on the buy or sell side regardless of supply and demand. if Harn started SELLING Q300 swords from his infinite stockpile for 5,000 tria each then crafters would not be able to sell for any more than that because Harn would be undercutting them.
The example I gave was simple for the sake of explaining the concept. Yes, you can add all sorts of logic to try and counter manipulation but you cannot eliminate it altogether. If you look at modern stock markets, you will see that there are people who's job it is to monitor the market for manipulation, to investigate and prosecute those who do so. Do you think Planeshift has the resources to do that? NO.
Also, What you mentioned about being suspicious of inflated prices is not that easy. To do that you need some point of reference. You could say that the npc should be wary of price changes in excess of %10 of the previous day's average .. but that would only lead to slower manipulation over the course of weeks or months... and smaller windfalls. It would also put the NPC out of line should the value of an item actually change that much. If steel mining was suddenly disabled due to a bug, and there was a strong demand for crafted weapons, the value of steel would go up and so too would the value of swords. If the NPC thought this was nonsense based on historical prices, he might be left in an exploitable state because his prices are not current.
If you give the NPC a FIXED supply of goods to sell, then players could deplete the NPC's reseve and then take over the market - charging any price the choose... that would be very bad.