My (sample size 2) theory is that USB-C isn't the best connector for a security key, since it intentionally moves the wear-prone part (i.e. the dust-collecting and mechanical spring involving side) from the port to the cable.
USB-A is completely solid state, and most security keys use the "flat" variant of the plug that further reduces the chance of mechanical damage and/or collecting dust.
Looking at all of my USB-C keys, most of them get visibly bent inwards after a couple of years of carrying them in a pocket on a keychain with other keys.
It's hard to imagine a USB-A key breaking in the same way. The only thing that could conceivably break it is the PCB itself snapping, or possibly static electricity (but I don't know how much better USB-C keys would fare in that regard).
So given that I can buy 2-3 A-to-C adapters for the price difference between a USB-A and a USB-C key, why take the additional risk?
Type A is more durable, for sure.
But on the PC side, my old HP laptop used to have extremely tight USB A ports. I'd have to pull ridiculously hard on cables to disconnect them. Now the ports are fairly loose, to the point that my external drive sometimes disconnects...
The yubikey kinda dances around in that port. Luckily, I don't move the laptop too much, so the key tends to stay put, but it sometimes does lose contact out when I need to touch it often.