Scarce / non-renewable items

Solution 1:

The inventory of merchants does respawn after a while, you have to meditate for about 24-48 hours and there should be a new selection of stuff to buy. I used that to get enough iron and silver ore for some swords, as the shop did not sell enough of the ore at once to craft the new sword.

Plants also do respawn after a short while, those you also can farm indefinitely. I'm not sure if you can get every single alchemy ingredient everywhere just from plants and respawning monsters, but there is usually an alchemy shop in every area so you should be able to buy anything you're missing. Except for certain quests, you only need the 9 base alchemy types, you don't need any specific ingredients, just something that e.g. contains Quebrith.

So, as long as you have enough money and the merchants generally stock the items you need, you shouldn't run out of crafting ingredients.