In the original release of Ego Draconis it wasn't too hard to get 3 gems with moderate reloading, and 4 with a lot of reloading or getting very lucky (I think I only got 4 once).
In the Dragon Knight Saga / Developer's Cut, though, those numbers drop by 1. After trying a fair bit to get 3 gems on the first malachite vein, I put a time limit on reloading, and would generally take 2 as good enough.
In the Flames of Vengeance section of the game, any quest that gives gems has a chance to give malachite gems (3 or 5, depending on the quest). I usually reloaded a few times to see if I could get malachite, but had a time limit.
I acquired about 30 malachite gems in the D2:ED section of the game (used a couple for healing auras on jewellery and 2 for Simeon), and at the end of the game had 65. If I play again, I'm going to have to be less stingy using level 10 enchantments and healing auras, or not bother reloading for malachite veins or FoV quests.