I think they should go away, and all their fixtures made available through the crafting system. Here is my reasoning:
1) None of the fixtures have any good, plausible in-character explanation as to why they cannot be simply made by the PC. Why can’t a smith make a bird cage with wrought-iron? Why is an alchemist unable to manage a blue ritual circle as opposed to a red one?
2) Their rarity makes them a prime target for thieves, thus ensuring that they rarely get used for fear of them being taken by quarterbreakers in favor of an easy flip. Think for a bit. When’s the last time you’ve seen any of the fixtures produced by the pigments in a public place?
3) There are plenty of other things that you can get through sailing, rare treasures that you can acquire for your character, that I doubt sailors would be too tore up over this change.