I think those items are randomly mixed with other items, I recall getting some Nightshade when I harvested Deep Mushroom a couple of times. Bloodmoss? I am not sure of, I don't think I ever found bloodmoss yet.
Blood Moss is found with Red Mandrake - pretty much only in Wizard City (there are a couple of spawns in Grizzleheim, but not worth trying to get to at lower levels). Nightshade is found with Deep Mushroom all over the Spiral. This is probably the most common "Rare" reagent. Transmute recipes are available for both of these, the Blood Moss one can be purchased from Eudora in Olde Town, and Nightshade from Wul'yahm in the Oasis.