I tried overclocking on my pc but didn't notice anything. It's weird. Maybe the game itself just uses less frames for jumping/projectiles. The player can smoothly move left/right while at the same time an enemy can throw a projectile at a lower framerate. The whole game doesn't slow down.
Please do not post a support request without first reading and following the advice in https://retropie.org.uk/forum/topic/3/read-this-first