1. My stockpiles are slowly filling with Dragon, Forgotten Beast and Crundle Scales. These are useless? Can't be used for anything?
Completely useless in vanilla.
2. They can be used - for leather armour - by modding the RAWs, but this needs a new world to be gen'd?
They can be used for a few things. The easiest way to use them is to add the [SHELL] tag to the scale material template. This lets you use scale as shells in decoration and moods, but if you tell a bonecrafter to make shell crafts you'll get things like 'crundle scale large gem' appearing for some reason. This can be done to an existing world.
You can also modify scale to count as skin for leather. To do this you need to modify scale to have the appropriate tag to use the standard tanning reaction, and then you need to go through every creature in the raws that has scales and remove the line that removes leather from that creature. I think this can be done post-worldgen, but I haven't tried applying this mod to a world that already exists.
3. Ditto for alpaca, sheep, etc. wool. These are the leftovers from "incidental" corpses, ie. animals that weren't butchered in time. (I think) These'll never be used for spinning, etc, right?
Wool that has been sheared from a living animal can be used, but wool left over from butchering will usually be too short to be spun into cloth. Sometimes it will work, sometimes it won't. Your doctor can still use it to suture wounds.