Honey is deliberately surfaceside.
Garlic comes from mainly the Tinkers, as far as I've been aware - I've not seen any plants with it.
Ancient Softwood, for some reason, seems to be incredibly rare (or I'm not touching the right writs).
Flameberries are only from the Burning Shores.
Weirdly, do Flame Beetle Bellies, which are used for a one/use summon item that's entirely outclassed by the time you reach there. Adding those to the Sewers would be super helpful.
Some plants only grow in the Spore Farms; Mintspear, Lady's Tear, if you're underground. A big problem is the Spore Farms are a district lock - which can limit who can access things. This means that if they are slaves or part of the wrong district, you can't get things like Lady's Tear or Mintspear. UDers also can't buy from Azoun, as well as spices, rice, kaeth, etc - everything is locked there.
Mandrake roots are also Spore Farms exclusive below, that I've seen
Sailfin, Eagle Feathers are more important thanks to being needed for Gravity items, but neither spawn anywhere in the UD that I've seen
Zinc is rare, but that's everywhere! Mithril seems very common (to the extent steel can be harder to get hold of sometimes).