The sad part is moderate-sized ships (I won't say big ships, because that makes me think Type-9, Anaconda, etc) are the only ones with jump drives sufficient to make the trips reasonable, as far as I'm concerned. Type-6's drive, at least well-upgraded, allows for enough range to make a rare run in about a dozen jumps, maybe more, while most smaller ships would have to make twice to three times as many jumps, depending on their possible range, and would likely end up with even more roundabout routes. Maybe someone likes taking the 'scenic route', and that's their thing. They probably would have done that with or without the rare goods to trade. Even with the smaller ships that can get better range, they tend to have pretty good cargo capacity, as well, so even moderate amounts (in terms of cargo holds) would still be ideal.
In any case, as I've already said earlier, there's millions upon millions of tons of generic goods available in all parts of human-occupied space; it's not like the rare goods being available in a few dozen tons per player makes it any less 'rare'. Even if they were back to 100 ton spawn rates for the highest-spawning goods, that's still less than 0.1% of generic good counts, if I were to make a guess.
Lower the profits per ton, maybe, or increase the range required for best profits would have been better ways to nerf this, in my opinion. As for variance for different hold sizes, the game already had different spawn rates for different specialty/unique/rare commodities, so a ship like a Hauler could have gone after the ones that spawned in smaller numbers easily and probably made more per ton than, say, a Type-6 grabbing at least a mostly-full load from the larger-number spawning commodities.