Not a bug really, just a potential headache.
If a core sends a lot to stderr (try mGBA at level 0 (debug)), it can cause slowdown in KMS mode. Redirecting the stream to a log file or even just /dev/null puts solves the problem. Turning off logging verbosity solves the problem, though it’s probably best to just increase the level. This doesn’t happen when launching from bash or the fancy desktop icon.
Hopefully this helps someone, someday. Maybe it would be appropriate to set the default verbosity level to 1?