That's surprising to me; wouldn't they be able to represent huge chunks of world state as giant matrices, upon which operations are trivial to parallelize?

Yes, but most flight sims are based on very old codebases. X-Plane has started to change, and Prepar3d too, but I imagine they're so complicated it's difficult to just do without breaking a lot of things.

For the time being, even with latest versions, single-threaded cpu performance is the largest concern in these sims.