I haven't fallen below 1k+ of each crystal yet. When you level up every craft you get many crystals.
I noticed this as well. During phase 3, I had to constantly go out and gather crystals through mining or botany. However, they really increased the amount of shards given as part of the reward for completing the lvl 5/10/15/etc DoH quests.
Granted, I've only gotten up to around lvl 15, so I don't know if the higher amount of exp needed at later levels will require more shards than you get from quest rewards. Also, some crafts eat up shards more quickly than others (e.g. Weaving requires more intermediary steps to create ingredients than Leathercraft).
Lyonheart, like Eorzia, will be reborn in FFXIV!
FFXI veteran (Lyonheart and Lakiskline of Lakshmi)
1/467 on signed HQ Weskit!!!