Wait, NPCs restock over time? I thought it was only on level up. Either way, I don't see that as a problem. More overall choices if you happen to be stuck on a level for a while.
Making "skill mules" is something kind of like savescumming: if people want to do it, okay, but don't complain if that cheesy tactic makes the economy problematic. Larian could fix this somehow, but it could be a limitation on people who actually want to hire different henchman to try different strategies out and stuff. Larian should focus on balancing things that every player does, not things that are basically exploits (you're exploiting a henchman for his barter skills! You should pay him at least!) I'm not sure the exact percentages barter gives, but they're probably too high. In Wasteland 2, a point in Barter gives you a whopping 1% decrease in price costs and increase in player sell values. That's too low for DOS, but I think it shouldn't actually be that much higher than that. Perhaps 3 or 4% a point. That 15-20% shift would be useful, but not absurd like it is now.
I suppose you can make unlimited money with crafting if NPCs really do restock every few hours. I think there's a balance to be had here: crafting should be a possible source of income, but it shouldn't provide ridiculous amounts of wealth. I guess if someone wants to wait around for a restock and craft to make even a meager amount of money several times, they can bore themselves to death with that.
As far as your last point, that would be less of an issue if money was a concern and other traders had more good items in general.
