I'd say, just remove weapons, armor and tools from traders. Not for sale, not for quest rewards. You want rank 6 weapons armor and tools? Make them findable when you hit certain loot stages. Otherwise, no finding any weapons, armor, or tools rank 2, 3, 4 or 5.
Is this a perfect solution? Probably not. But it'd at least make crafting those types of items, and thus their magazines, worth getting.