I come back and play a new character after over a year away, and I'm barely averaging 6 Warm Fire Crystals for an entire run of 3-2 Shadow of the Beast. When I used to see crystals drop from 1 out of 4 prize boxes on missions like 6-2 Sewer Stash, Terminal Meltdown, and Soverign Slime, now it's often the case that I get none at all from an entire floor, even from a dozen boxes. And I'm playing on Elite.
Were crystal drop rates altered in the last year or something?
The big data sets (for example, here) are a few years old now. There doesn't seem to be much recent data to confirm or refute what you're saying.
In lieu of data, here are anecdotes. A full Tier-3 run used to earn about 12 5-star fire crystals, and recently I've been earning around that. And 5-star orbs of alchemy still show up pretty regularly. So it seems that drop rates have not changed in Tier 3. I know less about Tier 2.