With clouds (130-140fps):

Without clouds (160-170fps):

I use a 165hz monitor, so I did actually notice this without checking F3 😆

I see you draw each face individually like in Vanilla: https://github.com/misterslime/fabulousclouds-fabric/blob/300f6504e2dbc1291e387eee6c43d27258077e6f/src/main/java/net/misterslime/fabulousclouds/mixin/MixinLevelRenderer.java#L213-L214

Perhaps you could perform some meshing to reduce the amount of vertices rendered? You could even write your own shader that only uses 2 bits per vertex and a global color to control the different directional colors. It might even be faster than Vanilla cloud rendering at that point!