I've noticed when emulating the 3DS and Wii U that precompiled shaders run faster than just generally playing the game. Moreso on the Wii U than 3DS.
When playing something like Breath of the Wild, it generally runs slower, especially while it's configuring the shaders while I'm playing. However, if I come back to an area that uses the same shaders, it runs perfectly smooth.
3DS is less noticeable since it's a weaker system, but I can easily tell the difference. In general, my emulation settings overclock the 3DS CPU to make it run faster, generally because the more power I give it the better it runs. However, if I have all of the shaders there, I can revert the clock speed to normal, and it runs perfectly.
Does anyone know why precompiled shaders work faster than normal gameplay?
EDIT: In case you were wondering, this is all done legally.