My justification is that if you sell something in fewer quantity, it appears more precious to the buyer and they're willing to pay more for it.
In my opinion, merits are, ultimately, an abstraction of how well, or poorly, a Power is tending to the needs of a system as a whole. The “high profits” source of good merits are, in my opinion, as silly as rares, since they are usually luxury items, and a quick Look at a station’s commodity market typically shows that the people served by that market are starving, their factories are closed due to lack of materials and excessive inventory, and their people sick due to a lack of medicine.
It would make a ,or more sense, IMO, for commodities in high demand to produce the most merits, regardless of their profitability. On the flip side, when undermining, selling low supply commodities on a market is much is a much better way to ensure unrest, because below-cost imports kills local jobs.