I had 22 malachite gems before the hall of echoes, after giving 2 to the blind philosopher and using 4 throughout the game for level 10 healing aura enchantments (which require a malachite gem at any level).
Malachite veins should always have a malachite gem. It is relatively easy to get 1 or even 2 gems by reloading (3 or 4 require patience or luck), but not everyone is going to want to do so.
