While I cannot offer up any absolute evidence to the matter, I believe some of my crafting materials are disappearing, expiring or just plain going missing. I definitely use the shiz out of glyphs of the guardian, but it and runes of shattering are just about the only materials I ever do use.
That being said, after 160+ hours of play, the runes and glyphs I have accumulated seem to be disappearing. Not from use, but just from… playing the game? Like I said, I can not say for sure what is going on or if anything is actually happening, but I could have sworn at one point I had close to 200 runes of stability, but now I have only 50 or so. I only ever recall even having used one of those and that was to see what it did (once when I started playing and again when that particular run e was patched… to see how it changed.)
As for actual shards, sometimes shards of which I have several hundred (e.g. Health Added; suffix) appear to only number in the single digits. It does seem that logging out and back into the game “fixes” this back up to a somewhat expected number, but one can never be sure if it is accurate or if shards were lost (or perhaps never truly accrued.)
FWIW, this may all be in my head and I am way off the mark, but I do feel as if something is off regarding crafting material logistics/maintenance.