I don't think there's much of an issue with bots affecting crystals. It's just shards IMO.

I was killing time before going to an unspoiled node, and stopped to farm some earth crystals. I used the 2 extra crystals ability and got 12 from one node. At the time they were selling for almost 100gil each. That's MUCH better profit than I got from the unspoiled node. I also grabbed some pigment for dye that I sold 40 X 750gil. Again, way better than what I got in more time and effort from the unspoiled node.