“Use threaded video driver. Using this might improve performance at possible cost of latency and more video stuttering.” – in earlier retropie versions it was on by default. It was switched off for v3, but it turned out it affected performance on the rpi more than we thought, so it is back on again for new installs – for existing configs, you can configure it from the “configuration editor”
If you notice performance issues with an emulator, you can try switching it in all/retroarch.cfg or on a per system basis.