I'm currently working through completing the crafting log for shiny tools, compiled the requirements for weaver for level55-59 items that I hadn't crafted before. There are 31 of them and I require 1932 clusters/shards/crystals, 1142 of which are lightning crystals. This also includes needing to craft pre-requisite items such as Ramie Thread/Cloth, Hallowed Water etc. This works out an average of 62 per finished craft.

I currently sit at 5k of every crystal/shard/cluster but even I feel that a dent of 1142 just to fill in 5 levels of log is hefty. Hefty enough to be sending my retainers out to get me more crystals so I don't have such a discrepancy between these and the others.

My guess is you're probably not crafting all that much, or you're buying half the stuff from the marketboard and skipping a lot of pre-requisite crafting which seems to take up most of the shards/crystals/clusters.
Or you're simply going through a lot of passive ways (ie not gathering from a node) of getting yours, such as desynthesis or aetherial reduction.